???global.info.a_carregar???
Identification

Personal identification

Full name
Maria João Ramos
Gender
Female

Citation names

  • Ramos, Maria João
  • Maria J. Ramos
  • Ramos, Maria

Author identifiers

Ciência ID
781C-8592-F117
ORCID iD
0000-0002-7554-8324

Email addresses

  • mjramos@fc.up.pt (Professional)

Knowledge fields

  • Exact Sciences - Chemical Sciences
  • Natural sciences - Biological Sciences - Biochemistry
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
Education
Degree Classification
2014/09/30
Concluded
 Honorary Doctorate (Doctor)
Stockholms Universitet, Sweden
2000
Concluded
 Chemistry (Título de Agregado)
Universidade do Porto Faculdade de Ciências, Portugal
1991
Concluded
 Chemistry (Pós-doutoramento)
University of Oxford, United Kingdom
1983
Concluded
 Chemistry (Doutoramento)
University of Glasgow, United Kingdom
1977
Concluded
 Chemistry (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal
Affiliation

Teaching in Higher Education

Category
Host institution 		Employer
2010 - Current Full Professor (University Teacher) Universidade do Porto Faculdade de Ciências, Portugal
1989 - 2010 Associate Professor (University Teacher) Universidade do Porto Faculdade de Ciências, Portugal
1984 - 1989 Assistant Professor (University Teacher) Universidade do Porto Faculdade de Ciências, Portugal
1979 - 1984 Assistant (University Teacher) Universidade do Porto Faculdade de Ciências, Portugal

Positions / Appointments

Category
Host institution 		Employer
2014/06/27 - 2018/06/27 Vice-Rector Universidade do Porto, Portugal
2014/06/27 - 2018/06/27 Diretor UPTEC Associação de Transferência de Tecnologia da Asprela, Portugal
2009/03/25 - 2012/03/25 President of Department Universidade do Porto Faculdade de Ciências, Portugal
2000 - 2010 Associate Director National Foundation for Cancer Research, United States
Projects

Grant

Designation Funders
2022/12/18 - 2028/12/18 Center for enzymatic deconstruction of thermoset plastics for a sustainable society
DKK 57,003,755
PI in Portugal
Novo Nordisk Fonden, Denmark
Ongoing
2023 - 2024 Biodegrading unsaturated polyesters
EuroHPC - proposal No. EHPC-REG-2023R03-163

Contract

Designation Funders
2021/03/29 - 2024/12/28 Murderous Venom - Towards a Universal Antidote Against Snakebite
PTDC/QUI-OUT/1401/2020
10.54499/PTDC/QUI-OUT/1401/2020
co-PI
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

REQUIMTE LAQV Porto, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2023/06/01 - 2024/06/30 Biodegrading unsatured polyesters - establishing the enzymatic catalytic mechanism of Pseudomonas sp. MIS38 lipase
2022.15579.CPCA.A2
10.54499/2022.15579.CPCA.A2
Universidade do Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2018/10/01 - 2022/09/30 New Biocatalysts for Green Crude Oil Desulfurization
PTDC/QUI-QFI/28714/2017
PTDC/QUI-QFI/28714/2017
Researcher
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal

REQUIMTE LAQV Porto, Portugal
Fundação para a Ciência e a Tecnologia

Fundação para a Ciência e a Tecnologia
Concluded
2018/07/01 - 2021/06/30 RDB-TS: Uma base de dados de reações químicas baseadas em informação de estados de transição derivados de cálculos quânticos.
PTDC/QUI-QFI/31689/2017
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2019 - 2020 Bacterial Initiation factors and Termination factors as new targets to novel antibiotics
2018184467
2018184467
Principal investigator
Universidade do Porto Faculdade de Ciências, Portugal
 Partnership for Advanced Computing In Europe
Concluded
2019 - 2020 Local and collective motions as a gateway to the catalytic power of enzymes
CHM150-2019
CHM150-2019
Principal investigator
Universidade do Porto Faculdade de Ciências, Portugal
 Oak Ridge National Laboratory
Concluded
2015 - 2020 TCCM - Theoretical Chemistry and Computational Modelling
ITN-EJD-642294
Principal investigator
Universidade do Porto Faculdade de Ciências, Portugal
 European Union
Concluded
2016 - 2019 New Technologies for three Health Challenges of Modern Societies: Diabetes, Drug Abuse and Kidney Diseases
NORTE-01-0145-FEDER-000024
Principal investigator
REQUIMTE LAQV Porto, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Concluded
2015 - 2019 NatChemDrugs - Challenging Organic Syntheses Inspired by Nature: from Natural Products Chemistry to Drug Discovery
European Project CM1407
Researcher
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 European Union
Concluded
2014 - 2019 Aldehyde Oxidases in Drug Metabolism and Biocatalysis: Searching for the Substrate Specificity and Catalytic Mechanism
PTDC/BBB-BEP/1185/2014
PTDC/BBB-BEP/1185/2014
Researcher
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2013/01/01 - 2018 ENZYMATIC CATALYSIS - seeking a global picture
info:eu-repo/grantAgreement/FCT/COMPETE/128544/PT
EXCL/QEQ-COM/0394/2012
Principal investigator
REQUIMTE LAQV Porto, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal

Universidade do Porto Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia

Fundação para a Ciência e a Tecnologia
Concluded
2013 - 2015 Chelators for novel therapeutic strategies
NORTE-07-0124-FEDER-000066
NORTE-07-0124-FEDER-000066
Researcher
REQUIMTE LAQV Porto, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Concluded
2012/05/01 - 2014 New drugs for hypertension
info:eu-repo/grantAgreement/FCT/COMPETE/121744/PT
PTDC/QUI-QUI/121744/2010
Principal investigator
REQUIMTE LAQV Porto, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Universidade do Porto Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia

Fundação para a Ciência e a Tecnologia
Concluded
2010 - 2014 CODECS: COnvergent Distributed Environment for Computational Spectroscopy
European Project oc-2009-2-5734
European Project oc-2009-2-5734
Researcher
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 European Union
Concluded
2010 - 2014 Molecular machineries for ion translocation across biomembranes
European Project CM0902
European Project CM0902
Researcher
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 N/A
Concluded
2010 - 2014 Developing on-the-fly quantum dynamics for proton transfer in enzyme catalysis
Leverhulm Trust
Researcher
Concluded
2010/06/01 - 2013/09/30 New Biomolecular Force Field
PTDC/QUI-QUI/103118/2008
PTDC/QUI-QUI/103118/2008
Principal investigator
Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Universidade do Porto, Portugal

Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
Fundação para a Ciência e a Tecnologia

Fundação para a Ciência e a Tecnologia
Concluded
2010 - 2013 An innovative methodology to calculate drug-receptor binding free energies
PTDC/QUI-QUI/100372/2008
PTDC/QUI-QUI/100372/2008
Researcher
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2009/01/02 - 2012/06/30 Novas Arquitecturas Moleculares para Combater Processos Infecciosos
PTDC/QUI/67915/2006
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal

Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010 - 2012 Molecular Mechanisms of Hypercholesterolemia: New insights and New Therapeutic Strategies
PTDC/QUI-QUI/102760/2008
Researcher
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2009/01/02 - 2011 Novel Key Molecular Architectures to Target Infection
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/67915/PT
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2008 - 2010 Drug design towards the HIV-1 virus
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/68302/PT
Researcher
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluded
2008 - 2010 Uma abordagem complementar por Cristalografia de Raios-X, RMN e Química Computacional para a compreensão dos mecanismos de reconhecimento e ligação de substratos em módulos proteicos de ligação a polissacáridos
PTDC/QUI/68286/2006
PTDC/QUI/68286/2006
Researcher
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2008 - 2010 Estudos Espectroscópicos e Computacionais do Mecanismo Catalítico da Redutase do Nitrato
PTDC/QUI/67052/2006
PTDC/QUI/67052/2006
Researcher
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2005/01/01 - 2008/06/30 Enzymatic catalysis: mechanistic studies of cancer-related human enzymes
POCI/QUI/61563/2004
Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Universidade do Porto Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2006 - 2008 High-performance parallel computer facility for computational chemistry at the Associated Laboratory REQUIMTE
REEQ/1236/QUI/2006
REEQ/1236/QUI/2006
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
2005 - 2008 Catálise Enzimática: Estudos Mecanísticos de Enzimas Humanas Relacionadas com o Processo Cancerígeno
POCTI/QUI/61563/2004
Principal investigator
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2005 - 2008 MODELAÇÃO MOLECULAR E SÍNTESE DE PÉPTIDOS BIOACTIVOS
POCTI/QUI/55673/2004
Researcher
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2006 - 2007 Comparative Binding Energy Studies on Balanol Analogues As Inhibitors of Cyclic-AMP Dependent Protein Kinase: Development of HIV-Gene Expression Inhibitors By Targeting the Activation of Nuclear Factor – Kappa B
Luso-Spanish Agreement NºE-26/06
Principal investigator
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2004 - 2007 Infraestrutura de Cálculo Paralelo de Alta Performance para Química Computacional no Laboratório Associado REQUIMTE
CONC-REEQ/1236/2001
CONC-REEQ/1236/2001
Principal investigator
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
1998 - 2005 Estudo teórico do comportamento de ácidos monopróticos em solventes mistos água/álcool
PRAXIS/P/QUI/11302/98
PRAXIS/P/QUI/11302/98
Researcher
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2000 - 2003 Modelação de Mecanismos de Inibição em Radicais Enzimáticos: Uma proposta QM/CM
POCTI/35376/QUI/2000
POCTI/35376/QUI/2000
Principal investigator
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
1996 - 2002 Estudos de Adsorção sobre Superfícies Metálicas: uma Abordagem Teórica
PRAXIS/PCEX/C/QUI/61/96
PRAXIS/PCEX/C/QUI/61/96
Researcher
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2018/01/01 - 2021/12/31 NEW BIOCATALYSTS FOR GREEN CRUDE OIL DESULFURIZATION
PTDC/QUI-QFI/28714/2017
Co-PI
REQUIMTE LAQV Porto, Portugal

Universidade do Porto Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia
Outputs

Publications

Book
  1. Brás, N.F.; Cerqueira, N.M.F.S.A.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. Protein ligand docking in drug discovery. 2014.
    10.1007/978-3-319-09976-7_11
  2. Ramos, M.J.; Melo, A.; Henriques, E.S.; Ramos, MJ; Melo, A; Henriques, ES. Modelling enzyme - Ligand interactions. 2001.
Book chapter
  1. Maria Joao Ramos. "BOOK CHAPTERS - I have published 11 book chapters. For details please see www.fc.up.pt/pessoas/mjramos/BOOK _CHAPTERS.pdf". 2022.
  2. Teixeira, CSS; Fernandes, HS; Fernandes, PA; Ramos, MJ; Cerqueira, NMFSA. "Cancer therapies based on enzymatic amino acid depletion". 2017.
    10.1016/b978-0-323-46144-3.00024-6
  3. Sousa, Sergio F.; Coimbra, Joao T. S.; Fernandes, Pedro A.; Marino, Tiziana; Ramos, Maria J.; Russo, Nino; Nascimento, MAC; et al. "Molecular Dynamics Analysis of FAAH Complexed with Anandamide". 114-130. 2015.
    10.1007/978-3-319-14397-2_7
  4. Piekarski, D. G.; Ramos, M. J.; Diaz-Tendero, S.; Diaz, C; Rabadan, I; Garcia, G; Mendez, L; Martin, F. "Dynamics of excited clusters of beta-alanine in the gas phase". 2015.
    10.1088/1742-6596/635/3/032089
  5. Brás, NF; Coimbra, JTS; Neves, RPP; Cerqueira, NMFSA; Sousa, SF; Fernandes, PA; Ramos, MJ. "Computational Biochemistry". 2013.
    10.1016/b978-0-12-409547-2.10833-9
  6. Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ. "Ribonucleotide Reductase – Computational Studies". 2013.
    10.1007/978-3-642-16712-6_264
  7. Sousa, SF; Fernandes, PA; Ramos, MJ. "Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes". 2010.
    10.1007/978-90-481-3034-4_11
  8. Moreira, IS; Fernandes, PA; Ramos, MJ. "Computational Determination of the Relative Free Energy of Binding – Application to Alanine Scanning Mutagenesis". 2007.
    10.1007/1-4020-5372-x_6
Conference abstract
  1. Sousa, CF; Coimbra, JT; Ramose, MJ; Fernandes, PA; Gameiro, P; Ramos, MJ. "Combining theoretical and experimental approaches to understand the mechanism of antibiotic permeation: implications on the fight against bacterial resistance". 2019.
  2. Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ. "Enzyme Ribonucleotide Reductase. The Paradigm of Enzyme Inhibition by Furanone Derivatives". 2005.
    10.1107/s0108767305079511
Conference paper
  1. Medeiros, S; Fernandes, I; Nunes, J. "IDENTIFICATION OF ALKALI-SILICA REACTIONS IN SANTA MARIA ISLAND AIRPORT". 2014.
  2. dos Santos, PL; Ramos, JA. "Derivation of a bilinear Kalman filter with autocorrelated inputs". 2007.
    10.1109/cdc.2007.4434438
  3. dos Santos, PL; Ramos, JA; de Carvalho, JLM. "Identification of bilinear systems using an iterative deterministic-stochastic subspace approach". 2005.
    10.1109/cdc.2005.1583309
  4. Brito, NT; Ramos, MJ. "On-line classroom, a way of collecting information about students' skills". 2004.
Journal article
  1. Ribeiro, António J. M.; Fernandes, Pedro A.; Ramos, Maria J.. "Off the beaten (catalytic) path: Charting the mechanistic space of enzyme reactions". The Journal of Chemical Physics 163 13 (2025): https://doi.org/10.1063/5.0288283.
    10.1063/5.0288283
  2. Coimbra, João T. S.; Gissler, Antoine; Nitor, Emiel; Rostamipour, Kiana; Cunha, Ana V.; Ramos, Maria J.; Fernandes, Pedro A.. "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2-like Peptides". JACS Au 4 11 (2024): 4295-4306. https://doi.org/10.1021/jacsau.4c00646.
    10.1021/jacsau.4c00646
  3. Sousa, João P. M.; Ramos, Maria J.; Fernandes, Pedro A.. "The Catalytic Mechanism of Decarboxylation of L-DOPA to Dopamine by Papaver somniferum Aromatic Amino Acid Decarboxylase – A Computational Study". ChemCatChem 17 1 (2024): https://doi.org/10.1002/cctc.202400762.
    10.1002/cctc.202400762
  4. Sousa, João P. M.; Ramos, Maria J.; Fernandes, Pedro A.. "QM/MM Study of the Reaction Mechanism of L-Tyrosine Hydroxylation Catalyzed by the Enzyme CYP76AD1". The Journal of Physical Chemistry B 128 39 (2024): 9447-9454. https://doi.org/10.1021/acs.jpcb.4c05209.
    10.1021/acs.jpcb.4c05209
  5. Jerves, Carola; Neves, Rui P. P.; da Silva, Saulo L.; Ramos, Maria J.; Fernandes, Pedro A.. "Rate-enhancing PETase mutations determined through DFT/MM molecular dynamics simulations". New Journal of Chemistry 48 1 (2024): 45-54. https://doi.org/10.1039/d3nj04204a.
    10.1039/d3nj04204a
  6. João T. S. Coimbra; Pedro A. Fernandes; Maria J. Ramos. "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations". Journal of Chemical Information and Modeling (2023): https://doi.org/10.1021/acs.jcim.3c00962.
    10.1021/acs.jcim.3c00962
  7. Das, Sudip; Raucci, Umberto; Neves, Rui P. P.; Ramos, Maria J.; Parrinello, Michele. "How and When Does an Enzyme React? Unraveling a-Amylase Catalytic Activity with Enhanced Sampling Techniques". ACS Catalysis 13 12 (2023): 8092-8098. https://doi.org/10.1021/acscatal.3c01473.
    10.1021/acscatal.3c01473
  8. Castro-Amorim, Juliana; Oliveira, Ana; Mukherjee, Ashis K.; Ramos, Maria J.; Fernandes, Pedro A.. "Unraveling the Reaction Mechanism of Russell’s Viper Venom Factor X Activator: A Paradigm for the Reactivity of Zinc Metalloproteinases?". Journal of Chemical Information and Modeling 63 13 (2023): 4056-4069. https://doi.org/10.1021/acs.jcim.2c01156.
    10.1021/acs.jcim.2c01156
  9. Castro-Amorim, Juliana; Novo de Oliveira, Ana; Da Silva, Saulo Luís; Soares, Andreimar M.; Mukherjee, Ashis K.; Ramos, Maria João; Fernandes, Pedro A.. "Catalytically Active Snake Venom PLA2 Enzymes: An Overview of Its Elusive Mechanisms of Reaction". Journal of Medicinal Chemistry 66 8 (2023): 5364-5376. https://doi.org/10.1021/acs.jmedchem.3c00097.
    10.1021/acs.jmedchem.3c00097
  10. Ong, How Chee; Coimbra, João T. S.; Ramos, Maria J.; Xing, Bengang; Fernandes, Pedro A.; García, Felipe. "Beyond the TPP+“gold standard”: a new generation mitochondrial delivery vector based on extended PN frameworks". Chemical Science 14 15 (2023): 4126-4133. https://doi.org/10.1039/d2sc06508h.
    10.1039/d2sc06508h
  11. João T. S. Coimbra; Rui P. P. Neves; Ana V. Cunha; Maria J. Ramos; Pedro A. Fernandes. "Cover Feature: Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease (Chem. Eur. J. 42/2022)". Chemistry – A European Journal (2022): https://doi.org/10.1002/chem.202202001.
    10.1002/chem.202202001
  12. Amaral, LMPF; Moniz, T; Leite, A; Oliveira, A; Fernandes, P; Ramos, MJ; Araujo, AN; et al. "A combined experimental and computational study to discover novel tyrosinase inhibitors". JOURNAL OF INORGANIC BIOCHEMISTRY (2022):
    10.1016/j.jinorgbio.2022.111879
  13. Neves, RPP; Cunha, AV; Fernandes, PA; Ramos, MJ. "Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms". CHEMPHYSCHEM (2022):
    10.1002/cphc.202200159
  14. Viegas, MF; Neves, RPP; Ramos, MJ; Fernandes, PA. "QM/MM Study of the Reaction Mechanism of Thermophilic Glucuronoyl Esterase for Biomass Treatment". CHEMPHYSCHEM (2022):
    10.1002/cphc.202200269
  15. Coimbra, JTS; Neves, RPP; Cunha, AV; Ramos, MJ; Fernandes, PA. "Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease". CHEMISTRY-A EUROPEAN JOURNAL (2022):
    10.1002/chem.202201066
  16. Teixeira, LMC; Coimbra, JTS; Ramos, MJ; Fernandes, PA. "Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic". JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022):
    10.1021/acs.jcim.1c01561
  17. Sousa, CF; Coimbra, JTS; Richter, R; Morais-Cabral, JH; Ramos, MJ; Lehr, CM; Fernandes, PA; Gameiro, P. "Exploring the permeation of fluoroquinolone metalloantibiotics across outer membrane porins by combining molecular dynamics simulations and a porin-mimetic in vitro model". BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2022):
    10.1016/j.bbamem.2021.183838
  18. Neves, RPP; Ramos, MJ; Fernandes, PA. "Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis". JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022):
    10.1021/acs.jcim.2c01337
  19. Pinto, AV; Ferreira, P; Fernandes, PA; Magalhaes, AL; Ramos, MJ. "Development of Nanoscale Graphene Oxide Models for the Adsorption of Biological Molecules". JOURNAL OF PHYSICAL CHEMISTRY B (2022):
    10.1021/acs.jpcb.2c06037
  20. Neves, RPP; Fernandes, PA; Ramos, MJ. "Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by alpha-Amylase Explored with QM/MM Molecular Dynamics". JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022):
    10.1021/acs.jcim.2c00691
  21. Fernandes, PA; Passos, O; Ramos, MJ. "Necessity is the Mother of Invention: A Remote MolecularBioinformatics Practical Course in the COVID-19 Era br". JOURNAL OF CHEMICAL EDUCATION (2022):
    10.1021/acs.jchemed.1c01195
  22. Cordeiro, C; Borges, A; Ramos, MR. "A Strategy to Assess Water Meter Performance". JOURNAL OF WATER RESOURCES PLANNING AND MANAGEMENT (2022):
    10.1061/(asce)wr.1943-5452.0001492
  23. Fonseca, SM; Faria, S; Cunha, S; Silva, M; Ramos, MJ; Azevedo, G; Campos, R; Barbosa, AR; Queiros, C. "Mental health patterns during COVID-19 in emergency medical services (EMS)". INTERNATIONAL JOURNAL OF EMERGENCY SERVICES (2022):
    10.1108/ijes-08-2020-0052
  24. Pacheco, A; Monteiro, J; Santos, J; Sequeira, C; Nunes, J. "Energy transition process and community engagement on geographic islands: The case of Culatra Island (Ria Formosa, Portugal)". RENEWABLE ENERGY (2022):
    10.1016/j.renene.2021.11.115
  25. Hélio M. T. Albuquerque; Maria J. Ramos; Pedro Manuel Azevedo Alexandrino Fernandes; Artur M. S. Silva; Daniela Marisa Pinho Malafaia. "Chromeno[3,4-b]xanthones as first-in-class AChE and Aß aggregation dual-inhibitors". International Journal of Molecular Sciences (2021):
    Submitted
  26. Almeida, Cristina Ferreira; Teixeira, Natércia; Oliveira, Ana; Augusto, Tiago V.; Correia-da-Silva, Georgina; Ramos, Maria João; Fernandes, Pedro Alexandrino; Amaral, Cristina. "Discovery of a multi-target compound for estrogen receptor-positive (ER+) breast cancer: Involvement of aromatase and ERs". Biochimie 181 (2021): 65-76. http://dx.doi.org/10.1016/j.biochi.2020.11.023.
    10.1016/j.biochi.2020.11.023
  27. Brás, Natércia F.; Ferreira, Pedro; Calixto, Ana R.; Jaspars, Marcel; Houssen, Wael; Naismith, James H.; Fernandes, Pedro A.; Ramos, Maria J.. "Corrigendum: The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac". Chemistry – A European Journal 27 10 (2021): 3569-3569. http://dx.doi.org/10.1002/chem.202100062.
    10.1002/chem.202100062
  28. Coimbra, João T. S.; Feghali, Ralph; Ribeiro, Rui P.; Ramos, Maria J.; Fernandes, Pedro A.. "The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer". RSC Advances 11 2 (2021): 899-908. http://dx.doi.org/10.1039/d0ra09995c.
    10.1039/d0ra09995c
  29. Jerves, C; Neves, RPP; Ramos, MJ; da Silva, S; Fernandes, PA. "Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations". ACS CATALYSIS (2021):
    10.1021/acscatal.1c03700
  30. Ong, HC; Coimbra, JTS; Kwek, G; Ramos, MJ; Xing, BA; Fernandes, PA; Garcia, F. "Alkyl vs. aryl modifications: a comparative study on modular modifications of triphenylphosphonium mitochondrial vectors". RSC CHEMICAL BIOLOGY (2021):
    10.1039/d1cb00099c
  31. Neves, RPP; Ferreira, P; Medina, FE; Paiva, P; Sousa, JPM; Viegas, MF; Fernandes, PA; Ramos, MJ. "Engineering of PKS Megaenzymes-A Promising Way to Biosynthesize High-Value Active Molecules". TOPICS IN CATALYSIS (2021):
    10.1007/s11244-021-01490-5
  32. Bras, NF; Neves, RPP; Lopes, FAA; Correia, MAS; Palma, AS; Sousa, SF; Ramos, MJ. "Combined in silico and in vitro studies to identify novel antidiabetic flavonoids targeting glycogen phosphorylase". BIOORGANIC CHEMISTRY (2021):
    10.1016/j.bioorg.2020.104552
  33. Sousa, CF; Coimbra, JTS; Ferreira, M; Pereira Leite, C; Reis, S; Ramos, MJ; Fernandes, PA; Gameiro, P. "Passive Diffusion of Ciprofloxacin and its Metalloantibiotic: A Computational and Experimental study". JOURNAL OF MOLECULAR BIOLOGY (2021):
    10.1016/j.jmb.2021.166911
  34. Pinto, AV; Ferreira, P; Neves, RPP; Fernandes, PA; Ramos, MJ; Magalhaes, AL. "Reaction Mechanism of MHETase, a PET Degrading Enzyme". ACS CATALYSIS (2021):
    10.1021/acscatal.1c02444
  35. Faria, S; Fonseca, SM; Cunha, S; Silva, M; Ramos, MJ; Azevedo, G; Campos, R; Barbosa, AR; Queiros, C. "Predictors of COVID-19 Anxiety in Pre-Hospital Medical Emergency Professionals: Gender Differences". INTERNATIONAL JOURNAL ON WORKING CONDITIONS (2021):
    10.25762/ebmb-r373
  36. Ribeiro, J; Carneiro, I; Nuno, A; Porto, M; Edelaar, P; Luna, A; Reino, L. "Investigating people's perceptions of alien parakeets in urban environments". EUROPEAN JOURNAL OF WILDLIFE RESEARCH (2021):
    10.1007/s10344-021-01487-1
  37. Pinto, Alexandre V. Pinto; Oliveira, Ana N. L. Oliveira; Jerves, Carola Jerves; Mendonça, Filipa Lopes de Mendonça; Coutinho, Inês F. M. Coutinho; Coimbra, João T. S. Coimbra; Sousa, João P.M. Sousa; et al. "Proteínas Virais no Protein Data Bank". Revista de Ciência Elementar 8 2 (2020): http://dx.doi.org/10.24927/rce2020.022.
    Published • 10.24927/rce2020.022
  38. Ferreira, P; Cerqueira, NMFSA; Fernandes, PA; Romao, MJ; Ramos, MJ. "Catalytic Mechanism of Human Aldehyde Oxidase". ACS CATALYSIS (2020):
    10.1021/acscatal.0c02627
  39. Sousa, JPM; Neves, RPP; Sousa, SF; Ramos, MJ; Fernandes, PA. "Reaction Mechanism and Determinants for Efficient Catalysis by DszB, a Key Enzyme for Crude Oil Bio-desulfurization". ACS CATALYSIS (2020):
    10.1021/acscatal.0c03122
  40. Proenca, C; Oliveira, A; Freitas, M; Ribeiro, D; Sousa, JLC; Ramos, MJ; Silva, AMS; Fernandes, PA; Fernandes, E. "Structural Specificity of Flavonoids in the Inhibition of Human Fructose 1,6-Bisphosphatase". JOURNAL OF NATURAL PRODUCTS (2020):
    10.1021/acs.jnatprod.0c00014
  41. Sousa, SF; Calixto, AR; Ferreira, P; Ramos, MJ; Lim, C; Fernandes, PA. "Activation Free Energy, Substrate Binding Free Energy, and Enzyme Efficiency Fall in a Very Narrow Range of Values for Most Enzymes". ACS CATALYSIS (2020):
    10.1021/acscatal.0c01947
  42. Prejano, M; Medina, FE; Ramos, MJ; Russo, N; Fernandes, PA; Marino, T. "How the Destabilization of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase". ACS CATALYSIS (2020):
    10.1021/acscatal.9b04690
  43. Almada, M; Amaral, C; Oliveira, A; Fernandes, PA; Ramos, MJ; Fonseca, BM; Correia da Silva, G; Teixeira, N. "Cannabidiol (CBD) but not tetrahydrocannabinol (THC) dysregulate in vitro decidualization of human endometrial stromal cells by disruption of estrogen signaling". REPRODUCTIVE TOXICOLOGY (2020):
    10.1016/j.reprotox.2020.01.003
  44. Paiva, P; Ramos, MJ; Fernandes, PA. "Assessing the validity ofDLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions". JOURNAL OF COMPUTATIONAL CHEMISTRY (2020):
    10.1002/jcc.26401
  45. Sousa, R; Moorthy, NSHN; Fernandes, PA; Ramos, MJ; Bras, NF. "Binding Mode Prediction and Identification of New Lead Compounds from Natural Products as 3-OST Enzyme Inhibitors". LETTERS IN DRUG DESIGN & DISCOVERY (2020):
    10.2174/1570180817666200313105944
  46. Teixeira, CSS; Ramos, MJ; Sousa, SF; Cerqueira, NMFSA. "Solving the Catalytic Mechanism of Tryptophan Synthase: an Emergent Drug Target in the Treatment of Tuberculosis". CHEMCATCHEM (2020):
    10.1002/cctc.201901505
  47. Wilson, K. A.; Fernandes, P. A.; Ramos, M. J.; Wetmore, S. D.. "Exploring the Identity of the General Base for a DNA Polymerase Catalyzed Reaction Using QM/MM: The Case Study of Human Translesion Synthesis Polymerase eta". Acs Catalysis 9 3 (2019): 2543-2551. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000460600600086&KeyUID=WOS:000460600600086.
    10.1021/acscatal.8b04889
  48. Proenca, C.; Freitas, M.; Ribeiro, D.; Tome, S. M.; Oliveira, E. F. T.; Viegas, M. F.; Araujo, A. N.; et al. "Evaluation of a flavonoids library for inhibition of pancreatic alpha-amylase towards a structure-activity relationship". Journal of Enzyme Inhibition and Medicinal Chemistry 34 1 (2019): 577-588. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000457961100001&KeyUID=WOS:000457961100001.
    10.1080/14756366.2018.1558221
  49. Gameiro, P.; Sousa, C. F.; Coimbra, J. T. S.; Fernandes, P. A.; Ramos, M. J.. "Drug Permeation Across the Bacterial Membrane: Combining Theoretical and Experimental Approaches". Biophysical Journal 116 3 (2019): 206A-206A. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000460779801038&KeyUID=WOS:000460779801038.
    10.1016/j.bpj.2018.11.1138
  50. Puzzarini, C.; de Lara-Castells, M. P.; Ramos, M. J.. "Challenges in spectroscopy: accuracy versus interpretation from isolated molecules to condensed phases". Physical Chemistry Chemical Physics 21 7 (2019): 3395-3396. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000459585900001&KeyUID=WOS:000459585900001.
    10.1039/c9cp90025j
  51. Ribeiro, J; Branco, MC; Ribeiro, JA. "The corporatisation of football and CSR reporting by professional football clubs in Europe". INTERNATIONAL JOURNAL OF SPORTS MARKETING & SPONSORSHIP (2019):
    10.1108/ijsms-05-2017-0039
  52. dos Santos Moreira, CDD; Ribeiro Nunes Ramos, MJRN; Azevedo Alexandrino Fernandes, PMAA. "Glutamine synthetase structure-catalysis relationship-Recent advances and applications". WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2019):
    10.1002/wcms.1399
  53. Coimbra, JTS; Bras, NF; Fernandes, PA; Rangel, M; Ramos, MJ. "A computational study on the redox properties and binding affinities of iron complexes of hydroxypyridinones". JOURNAL OF MOLECULAR MODELING (2019):
    10.1007/s00894-019-4037-0
  54. Dalla Torre, G; Mujika, JI; Izabela Lachowicz, JI; Ramos, MJ; Lopez, X. "The interaction of aluminum with catecholamine-based neurotransmitters: can the formation of these species be considered a potential risk factor for neurodegenerative diseases?". DALTON TRANSACTIONS (2019):
    10.1039/c8dt04216k
  55. Ribeiro, J; Davids, K; Araujo, D; Silva, P; Ramos, J; Lopes, R; Garganta, J. "The Role of Hypernetworks as a Multilevel Methodology for Modelling and Understanding Dynamics of Team Sports Performance". SPORTS MEDICINE (2019):
    10.1007/s40279-019-01104-x
  56. Araujo, MP; Nunes, M; Rocha, IM; Pereira, MFR; Freire, C. "Electrocatalytic activity of new Mn3O4@oxidized graphene flakes nanocomposites toward oxygen reduction reaction". JOURNAL OF MATERIALS SCIENCE (2019):
    10.1007/s10853-019-03508-6
  57. Almada, M; Oliveira, A; Amaral, C; Fernandes, PA; Ramos, MJ; Fonseca, B; Correia da Silva, G; Teixeira, N. "Anandamide targets aromatase: A breakthrough on human decidualization". BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS (2019):
    10.1016/j.bbalip.2019.08.008
  58. Calixto, AR; Ramos, MJ; Fernandes, PA. "Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway". CHEMICAL SCIENCE (2019):
    10.1039/c9sc01464k
  59. Ferreira, P; Cerqueira, NMFSA; Coelho, C; Fernandes, PA; Romao, MJ; Ramos, MJ. "New insights about the monomer and homodimer structures of the human AOX1". PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2019):
    10.1039/c9cp01040h
  60. Ong, HC; Hu, Z; Coimbra, JTS; Ramos, MJ; Kon, OL; Xing, BG; Yeow, EKL; Fernandes, PA; Garcia, F. "Enabling Mitochondrial Uptake of Lipophilic Dications Using Methylated Triphenylphosphonium Moieties". INORGANIC CHEMISTRY (2019):
    10.1021/acs.inorgchem.8b03380
  61. Listyarini, RV; Gesto, DS; Paiva, P; Ramos, MJ; Fernandes, PA. "Benchmark of Density Functionals for the Calculation of the Redox Potential of Fe3+/Fe2+ Within Protein Coordination Shells". FRONTIERS IN CHEMISTRY (2019):
    10.3389/fchem.2019.00391
  62. Medina, FE; Ramos, MJ; Fernandes, PA. "Complexities of the Reaction Mechanisms of CC Double Bond Reduction in Mammalian Fatty Acid Synthase Studied with Quantum Mechanics/Molecular Mechanics Calculations". ACS CATALYSIS (2019):
    10.1021/acscatal.9b03531
  63. Prejano, M; Medina, FE; Fernandes, PA; Russo, N; Ramos, MJ; Marino, T. "The Catalytic Mechanism of Human Transketolase". CHEMPHYSCHEM (2019):
    10.1002/cphc.201900650
  64. Paiva, P; Sousa, SF; Fernandes, PA; Ramos, MJ. "Human Fatty Acid Synthase: A Computational Study of the Transfer of the Acyl Moieties from MAT to the ACP Domain". CHEMCATCHEM (2019):
    10.1002/cctc.201900548
  65. Fernandes, H. S.; Ramos, M. J.; Cerqueira, Nmfsa. "Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study". Acs Catalysis 8 11 (2018): 10096-10110. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000449723900021&KeyUID=WOS:000449723900021.
    10.1021/acscatal.8b02321
  66. Almeida, J. R.; Mendes, B.; Lancellotti, M.; Marangoni, S.; Vale, N.; Passos, O.; Ramos, M. J.; et al. "A novel synthetic peptide inspired on Lys49 phospholipase A(2) from Crotalus oreganus abyssus snake venom active against multidrug-resistant clinical isolates". European Journal of Medicinal Chemistry 149 (2018): 248-256. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000429186900022&KeyUID=WOS:000429186900022.
    10.1016/j.ejmech.2018.02.055
  67. Santos-Martins, D.; Calixto, A. R.; Fernandes, P. A.; Ramos, M. J.. "A Buried Water Molecule Influences Reactivity in a alpha-Amylase on a Subnanosecond Time Scale". Acs Catalysis 8 5 (2018): 4055-4063. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000431727300039&KeyUID=WOS:000431727300039.
    10.1021/acscatal.7b04400
  68. Viegas, M. F.; Neves, R. P. P.; Ramos, M. J.; Fernandes, P. A.. "Modeling of Human Fatty Acid Synthase and &ITin Silico&IT Docking of Acyl Carrier Protein Domain and Its Partner Catalytic Domains". Journal of Physical Chemistry B 122 1 (2018): 77-85. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000422814000008&KeyUID=WOS:000422814000008.
    10.1021/acs.jpcb.7b09645
  69. Coimbra, J. T. S.; Bras, N. F.; Fernandes, P. A.; Rangel, M.; Ramos, M. J.. "Membrane partition of bis-(3-hydroxy-4pyridinonato) zinc(ii) complexes revealed by molecular dynamics simulations". Rsc Advances 8 48 (2018): 27081-27090. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000445747800010&KeyUID=WOS:000445747800010.
    10.1039/c8ra03602k
  70. Barbosa, A. C. C.; Neves, R. P. P.; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Mechanistic Studies of a Flavin Monooxygenase: Sulfur Oxidation of Dibenzothiophenes by DszC". Acs Catalysis 8 10 (2018): 9298-9311. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000447224100036&KeyUID=WOS:000447224100036.
    10.1021/acscatal.8b01877
  71. Silva, A. M. N.; Coimbra, J. T. S.; Castro, M. M.; Oliveira, A.; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.; Rangel, M.. "Determining the glycation site specificity of human holo-transferrin". Journal of Inorganic Biochemistry 186 (2018): 95-102. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000441704600012&KeyUID=WOS:000441704600012.
    10.1016/j.jinorgbio.2018.05.016
  72. Simoes, I. C. M.; Coimbra, J. T. S.; Neves, R. P. P.; Costa, I. P. D.; Ramos, M. J.; Fernandes, P. A.. "Properties that rank protein: protein docking poses with high accuracy". Physical Chemistry Chemical Physics 20 32 (2018): 20927-20942. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000447367900018&KeyUID=WOS:000447367900018.
    10.1039/c8cp03888k
  73. Ferreira, P.; Cerqueira, Nmfsa; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Parametrization of Molybdenum Cofactors for the AMBER Force Field". Journal of Chemical Theory and Computation 14 5 (2018): 2538-2548. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000431926500023&KeyUID=WOS:000431926500023.
    10.1021/acs.jctc.8b00137
  74. Fernandes, H. S.; Ramos, M. J.; Cerqueira, Nmfsa. "molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software". Journal of Computational Chemistry 39 19 (2018): 1344-1353. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000434970500019&KeyUID=WOS:000434970500019.
    10.1002/jcc.25189
  75. Zuniga, M. A.; Alderete, J. B.; Jana, G. A.; Fernandez, P. A.; Ramos, M. J.; Jimenez, V. A.. "Modulation of lateral and longitudinal interdimeric interactions in microtubule models by Laulimalide and Peloruside A association: A molecular modeling approach on the mechanism of microtubule stabilizing agents". Chemical Biology & Drug Design 91 5 (2018): 1042-1055. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000430168300006&KeyUID=WOS:000430168300006.
    10.1111/cbdd.13168
  76. Gabriele Dalla Torre; Jon I. Mujika; Elena Formoso; Eduard Matito; Maria J. Ramos; Xabier Lopez. "Tuning the affinity of catechols and salicylic acids towards Al(iii): characterization of Al–chelator interactions". Dalton Transactions 47 29 (2018): 9592-9607. https://doi.org/10.1039%2Fc8dt01341a.
    10.1039/c8dt01341a
  77. Biernacki, K.; Sousa, S. F.; Gales, L.; Ramos, M. J.; Magalhaes, A. L.. "Transport Properties of Light Gases in Nanochannels of L-Leu-L-Ser Dipeptide Crystals: A Comparative Study by Molecular Dynamics Simulations". Chemistryselect 3 20 (2018): 5517-5525. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000433494600004&KeyUID=WOS:000433494600004.
    10.1002/slct.201800559
  78. Ramos, M. J.; Fernandes, P. A.. "Structure, Dynamics, and Energetics of ATP Hydrolysis by ABC Transporters". Acs Central Science 4 10 (2018): 1300-1302. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000448053200005&KeyUID=WOS:000448053200005.
    10.1021/acscentsci.8b00631
  79. Medina, F. E.; Neves, R. P. P.; Ramos, M. J.; Fernandes, P. A.. "QM/MM Study of the Reaction Mechanism of the Dehydratase Domain from Mammalian Fatty Acid Synthase". Acs Catalysis 8 11 (2018): 10267-10278. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000449723900039&KeyUID=WOS:000449723900039.
    10.1021/acscatal.8602616
  80. Friedman, R.; Khalid, S.; Aponte-Santamaria, C.; Arutyunova, E.; Becker, M.; Boyd, K. J.; Christensen, M.; et al. "Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology". Journal of Membrane Biology 251 5-6 (2018): 609-631. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000450567200001&KeyUID=WOS:000450567200001.
    10.1007/s00232-018-0050-y
  81. Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Visualizing the Microscopic World". Interdisciplinary Sciences-Computational Life Sciences 10 1 (2018): 105-110. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000426823400010&KeyUID=WOS:000426823400010.
    10.1007/s12539-017-0255-2
  82. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Understanding the Rate-Limiting Step of Glycogenolysis by Using QM/MM Calculations on Human Glycogen Phosphorylase". Chemmedchem 13 15 (2018): 1608-1616. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000441432700013&KeyUID=WOS:000441432700013.
    10.1002/cmdc.201800218
  83. Paiva, P.; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Understanding the Catalytic Machinery and the Reaction Pathway of the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase". Acs Catalysis 8 6 (2018): 4860-4872. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000434369600014&KeyUID=WOS:000434369600014.
    10.1021/acscatal.8b00577
  84. Gonzalo A. Jaña; Fernanda Mendoza; Manuel I. Osorio; Joel B. Alderete; Pedro A. Fernandes; Maria J. Ramos; Verónica A. Jiménez. "A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans". Organic & Biomolecular Chemistry 16 14 (2018): 2438-2447. https://doi.org/10.1039%2Fc8ob00284c.
    10.1039/c8ob00284c
  85. Corley, MFV; Ferreira, S; Grundy, D; Nunes, J; Pires, P; Rosete, J; Goncalves, AR; Mata, V. "New and interesting Portuguese Lepidoptera records from 2017 (Insecta: Lepidoptera)". SHILAP-REVISTA DE LEPIDOPTEROLOGIA (2018):
  86. Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation". Chemphyschem 19 6 (2018): 669-689. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000428380500001&KeyUID=WOS:000428380500001.
    10.1002/cphc.201700339
  87. Paiva, P.; Costa, I. P. D.; Ferreira, C. E.; Ferreira, P.; Pereira, A. T.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Studies on neuraminidase inhibition". International Journal of Quantum Chemistry 118 9 (2018): 13-13. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000428413300014&KeyUID=WOS:000428413300014.
    10.1002/qua.25592
  88. Bras, N. F.; Santos-Martins, D.; Fernandes, P. A.; Ramos, M. J.. "Mechanistic Pathway on Human alpha-Glucosidase Maltase-Glucoamylase Unveiled by QM/MM Calculations". Journal of Physical Chemistry B 122 14 (2018): 3889-3899. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000430641900020&KeyUID=WOS:000430641900020.
    10.1021/acs.jpcb.8b01321
  89. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.; Schwartz, S. D.. "Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations". Chemistry-a European Journal 24 8 (2018): 1978-1987. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000424226000031&KeyUID=WOS:000424226000031.
    10.1002/chem.201705090
  90. Araujo, MP; Nunes, M; Rocha, IM; Pereira, MFR; Freire, C. "Co3O4 Nanoparticles Anchored on Selectively Oxidized Graphene Flakes as Bifunctional Electrocatalysts for Oxygen Reactions". CHEMISTRYSELECT (2018):
    10.1002/slct.201802108
  91. Simoes, Ines C. M.; Costa, Ines P. D.; Coimbra, Joao T. S.; Ramos, Maria J.; Fernandes, Pedro A.. "New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces". Journal of Chemical Information and Modeling 57 1 (2017): 60-72. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000392687400008&KeyUID=WOS:000392687400008.
    10.1021/acs.jcim.6b00378
  92. Barra, Pabla A.; Ribeiro, Antonio J. M.; Ramos, Maria J.; Jimenez, Veronica A.; Alderete, Joel B.; Fernandes, Pedro A.. "Binding free energy calculations on E-selectin complexes with sLe(x) oligosaccharide analogs". Chemical Biology & Drug Design 89 1 (2017): 114-123. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000390354100010&KeyUID=WOS:000390354100010.
    10.1111/cbdd.12837
  93. Fernandes, H S; Silva Teixeira, C S; Fernandes, P A; Ramos, M J; Cerqueira, N M F S A. "Amino acid deprivation using enzymes as a targeted therapy for cancer and viral infections.". Expert opinion on therapeutic patents 27 3 (2017): 283-297. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:27813440&KeyUID=MEDLINE:27813440.
    10.1080/13543776.2017.1254194
  94. Medina, Fabiola E.; Neves, Rui P. P.; Ramos, Maria J.; Fernandes, Pedro A.. "A QM/MM study of the reaction mechanism of human beta-ketoacyl reductase". Physical Chemistry Chemical Physics 19 1 (2017): 347-355. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000391725300037&KeyUID=WOS:000391725300037.
    10.1039/c6cp07014k
  95. Cerqueira, N. M. F. S. A.; Moorthy, H.; Fernandes, P. A.; Ramos, M. J.. "The mechanism of the Ser-(cis)Ser-Lys catalytic triad of peptide amidases". Physical Chemistry Chemical Physics 19 19 (2017): 12343-12354. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000401640600062&KeyUID=WOS:000401640600062.
    10.1039/c7cp00277g
  96. Coimbra, Joao T. S.; Fernandes, Pedro A.; Ramos, Maria J.. "Revisiting Partition in Hydrated Bilayer Systems". Journal of Chemical Theory and Computation 13 5 (2017): 2290-2299. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000401221300036&KeyUID=WOS:000401221300036.
    10.1021/acs.jctc.6b01258
  97. Hu, Zhang; Sim, Ying; Kon, Oi Lian; Ng, Wai Har; Ribeiro, Antonio J. M.; Ramos, Maria J.; Fernandes, Pedro A.; et al. "Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy". Bioconjugate Chemistry 28 2 (2017): 590-599. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000394481700036&KeyUID=WOS:000394481700036.
    10.1021/acs.bioconjchem.6b00682
  98. Calixto, A. R.; Ramos, M. J.; Fernandes, P. A.. "Influence of Frozen Residues on the Exploration of the PES of Enzyme Reaction Mechanisms". Journal of Chemical Theory and Computation 13 11 (2017): 5486-5495. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000415911800027&KeyUID=WOS:000415911800027.
    10.1021/acs.jctc.7b00768
  99. Sousa, C. F.; Coimbra, J. T. S.; Ferreira, M.; Ramos, M. J.; Fernandes, P. A.; Gameiro, P.. "Exploring the permeation of free and copper-complexed fluoroquinolones across the bacterial membrane". European Biophysics Journal with Biophysics Letters 46 (2017): S269-S269. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000416406201481&KeyUID=WOS:000416406201481.
  100. Merski, M.; Moreira, C.; Abreu, R. M. V.; Ramos, M. J.; Fernandes, P. A.; Martins, L. M.; Pereira, P. J. B.; Macedo-Ribeiro, S.. "Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2". Cell Death & Disease 8 (2017): 10-10. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000414022900040&KeyUID=WOS:000414022900040.
    10.1038/cddis.2017.487
  101. Neves, Rui P. P.; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. "Mechanistic insights on the reduction of glutathione disulfide by protein disulfide isomerase". Proceedings of the National Academy of Sciences of the United States of America 114 24 (2017): E4724-E4733. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000403179300004&KeyUID=WOS:000403179300004.
    10.1073/pnas.1618985114
  102. Pereira, A. T.; Ribeiro, A. J. M.; Fernandes, P. A.; Ramos, M. J.. "Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases". International Journal of Quantum Chemistry 117 18 (2017): 12-12. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000406687800002&KeyUID=WOS:000406687800002.
    10.1002/qua.25409
  103. Sousa, Sergio Filipe; Ribeiro, Antnio J. M.; Neves, Rui P. P.; Bras, Natercia F.; Cerqueira, Nuno M. F. S. A.; Fernandes, Pedro A.; Ramos, Maria Joao. "Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms". Wiley Interdisciplinary Reviews-Computational Molecular Science 7 2 (2017): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000399013100004&KeyUID=WOS:000399013100004.
    10.1002/wcms.1281
  104. Ribeiro, Rui P.; Coimbra, Joao T. S.; Ramos, Maria J.; Fernandes, Pedro A.. "Diffusion of the small, very polar, drug piracetam through a lipid bilayer: an MD simulation study". Theoretical Chemistry Accounts 136 4 (2017): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000404246000001&KeyUID=WOS:000404246000001.
    10.1007/s00214-017-2073-3
  105. Moreira, C.; Ramos, M. J.; Fernandes, P. A.. "Clarifying the Catalytic Mechanism of Human Glutamine Synthetase: A QM/MM Study". Journal of Physical Chemistry B 121 26 (2017): 6313-6320. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000405253000004&KeyUID=WOS:000405253000004.
    10.1021/acs.jpcb.7b02543
  106. Nunes, M; Moura, C; Hillman, AR; Freire, C. "Novel hybrid based on a poly[Ni(salen)] film and WO3 nanoparticles with electrochromic properties". ELECTROCHIMICA ACTA (2017):
    10.1016/j.electacta.2017.04.010
  107. Proenca, C; Freitas, M; Ribeiro, D; Oliveira, EFT; Sousa, JLC; Tome, SM; Ramos, MJ; et al. "alpha-Glucosidase inhibition by flavonoids: an in vitro and in silico structure-activity relationship study". JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY (2017):
    10.1080/14756366.2017.1368503
  108. Ferreira, P; Sousa, SF; Fernandes, PA; Ramos, MJ. "Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives". CHEMISTRY-A EUROPEAN JOURNAL (2017):
    10.1002/chem.201704057
  109. Fernandes, H. S.; Ramos, M. J.; Cerqueira, Nmfsa. "The Catalytic Mechanism of the Pyridoxal-5 '-phosphate-Dependent Enzyme, Histidine Decarboxylase: A Computational Study". Chemistry-a European Journal 23 38 (2017): 9162-9173. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000404854700024&KeyUID=WOS:000404854700024.
    10.1002/chem.201701375
  110. Santos-Martins, Diogo; Fernandes, Pedro Alexandrino; Ramos, Maria Joo. "Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas". Journal of Computer-Aided Molecular Design 30 11 (2016): 1079-1086. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000391459000013&KeyUID=WOS:000391459000013.
    10.1007/s10822-016-9951-y
  111. Neves, Rui P. P.; Fernandes, Pedro A.; Ramos, Maria J.. "Unveiling the Catalytic Mechanism of NADP(+)-Dependent Isocitrate Dehydrogenase with QM/MM Calculations". Acs Catalysis 6 1 (2016): 357-368. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000367706800039&KeyUID=WOS:000367706800039.
    10.1021/acscatal.5b01928
  112. Bras, Natercia F.; Ferreira, Pedro; Calixto, Ana R.; Jaspars, Marcel; Houssen, Wael; Naismith, James H.; Fernandes, Pedro A.; Ramos, Maria J.. "The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac". Chemistry-a European Journal 22 37 (2016): 13089-13097. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000383763200022&KeyUID=WOS:000383763200022.
    10.1002/chem.201601670
  113. Moreira, Catia; Ramos, Maria J.; Fernandes, Pedro Alexandrino. "Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations". Chemistry-a European Journal 22 27 (2016): 9218-9225. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000380271100028&KeyUID=WOS:000380271100028.
    10.1002/chem.201600305
  114. Oliveira, Eduardo F.; Cerqueira, Nuno M. F. S. A.; Ramos, Maria J.; Fernandes, Pedro A.. "QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase". Catalysis Science & Technology 6 19 (2016): 7172-7185. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000384876400018&KeyUID=WOS:000384876400018.
    10.1039/c6cy00356g
  115. Moorthy, N. S. Hari Narayana; Sousa, Sergio F.; Ramos, Maria J.; Fernandes, Pedro A.. "Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery". Journal of Enzyme Inhibition and Medicinal Chemistry 31 6 (2016): 1428-1442. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000385270300073&KeyUID=WOS:000385270300073.
    10.3109/14756366.2016.1144593
  116. Sousa, Rui P.; Fernandes, Pedro A.; Ramos, Maria J.; Bras, Natercia F.. "Insights into the reaction mechanism of 3-O-sulfotransferase through QM/MM calculations". Physical Chemistry Chemical Physics 18 16 (2016): 11488-11496. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000374786300091&KeyUID=WOS:000374786300091.
    10.1039/c5cp06224a
  117. Sousa, Sergio F.; Sousa, Joana F. M.; Barbosa, Ana C. C.; Ferreira, Cleide E.; Neves, Rui P. P.; Ribeiro, Antonio J. M.; Fernandes, Pedro A.; Ramos, Maria Joao. "Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)". Journal of Physical Chemistry a 120 27 (2016): 5300-5306. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000379988900079&KeyUID=WOS:000379988900079.
    10.1021/acs.jpca.6b01536
  118. Oliveira, Eduardo Filipe; Santos-Martins, Diogo; Ribeiro, Antonio Meireles; Bras, Natercia Fernandes; Cerqueira, Nuno Sousa; Sousa, Sergio Filipe; Ramos, Maria Joao; Fernandes, Pedro Alexandrino. "HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015)". Expert Opinion on Therapeutic Patents 26 11 (2016): 1257-1272. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000386784000004&KeyUID=WOS:000386784000004.
    10.1080/13543776.2016.1216977
  119. Moreira, Catia; Ramos, Maria J.; Fernandes, Pedro A.. "Glutamine Synthetase Drugability beyond Its Active Site: Exploring Oligomerization Interfaces and Pockets". Molecules 21 8 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000382334600067&KeyUID=WOS:000382334600067.
    10.3390/molecules21081028
  120. Cerqueira, Nuno M. F. S. A.; Oliveira, Eduardo F.; Gesto, Diana S.; Santos-Martins, Diogo; Moreira, Catia; Moorthy, Hari N.; Ramos, Maria J.; Fernandes, P. A.. "Cholesterol Biosynthesis: A Mechanistic Overview". Biochemistry 55 39 (2016): 5483-5506. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000384842100001&KeyUID=WOS:000384842100001.
    10.1021/acs.biochem.6b00342
  121. Moorthy, N. S. Hari Narayana; Sousa, Sergio F.; Ramos, Maria J.; Fernandes, Pedro A.. "Binding mode of conformations and structure-based pharmacophore development for farnesyltransferase inhibitors". Medicinal Chemistry Research 25 7 (2016): 1340-1357. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000378573400006&KeyUID=WOS:000378573400006.
    10.1007/s00044-016-1578-y
  122. Gama, J; Dias, G; Couceiro, M; Passos, P; Davids, K; Ribeiro, J. "An ecological dynamics rationale to explain home advantage in professional football". INTERNATIONAL JOURNAL OF MODERN PHYSICS C (2016):
    10.1142/s0129183116501023
  123. Nunes, M; Fernandes, DM; Rocha, IM; Pereira, MFR; Mbomekalle, IM; de Oliveira, P; Freire, C. "Phosphomolybdate@Carbon-Based Nanocomposites as Electrocatalysts for Oxygen Reduction Reaction". CHEMISTRYSELECT (2016):
    10.1002/slct.201601370
  124. Fernandes, DM; Nunes, M; Araujo, MP. "Carbon Nanomaterials-based modified electrodes for Electrocatalysis". BOLETIN DEL GRUPO ESPANOL DEL CARBON (2016):
  125. Llinas, Paola; Chenon, Melanie; Quyen Nguyen, T.; Moreira, Catia; de Regibus, Annelie; Coquard, Aline; Ramos, Maria J.; et al. "Structure of a truncated form of leucine zipper II of JIP3 reveals an unexpected antiparallel coiled-coil arrangement". Acta Crystallographica Section F-Structural Biology Communications 72 (2016): 198-206. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000371619200006&KeyUID=WOS:000371619200006.
    10.1107/s2053230x16001576
  126. Moniz, T.; Coimbra, J. T. S.; Bras, N. F.; Cunha-Silva, L.; Ramos, M. J.; Fernandes, P. A.; de Castro, B.; Rangel, M.. "Synthesis and structural characterization, by spectroscopic and computational methods, of two fluorescent 3-hydroxy-4-pyridinone chelators bearing sulphorhodamine B and naphthalene". Rsc Advances 6 5 (2016): 4200-4211. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000369508800094&KeyUID=WOS:000369508800094.
    10.1039/c5ra23217a
  127. Sousa, Sergio F.; Ramos, Maria J.; Lim, Carmay; Fernandes, Pedro A.. "Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases". Acs Catalysis 5 10 (2015): 5877-5887. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000362391500023&KeyUID=WOS:000362391500023.
    10.1021/acscatal.5b00923
  128. Shi, Y. X.; Liang, R. Z.; Martin, K. A.; Weston, N.; Gonzalez-Calera, S.; Ganguly, R.; Li, Y. X.; et al. "Synthesis and Hydrolytic Studies on the Air-Stable (4-CN-PhO)(E)P(mu-(NBu)-Bu-t) (2) (E = O, S, and Se) Cyclodiphosphazanes". Inorganic Chemistry 54 13 (2015): 6423-6432. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000357705800044&KeyUID=WOS:000357705800044.
    10.1021/acs.inorgchem.5b00735
  129. Oliveira, Bruno L.; Morais, Mauricio; Mendes, Filipa; Moreira, Irina S.; Cordeiro, Carlos; Fernandes, Pedro A.; Ramos, Maria J.; et al. "Re(I) and Tc(I) Complexes for Targeting Nitric Oxide Synthase: Influence of the Chelator in the Affinity for the Enzyme". Chemical Biology & Drug Design 86 5 (2015): 1072-1086. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000365404100013&KeyUID=WOS:000365404100013.
    10.1111/cbdd.12575
  130. Cerqueira, Nmfsa; Gesto, D.; Oliveira, E. F.; Santos-Martins, D.; Bras, N. F.; Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Receptor-based virtual screening protocol for drug discovery". Archives of Biochemistry and Biophysics 582 (2015): 56-67. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000360781200007&KeyUID=WOS:000360781200007.
    10.1016/j.abb.2015.05.011
  131. Pinto, G. P.; Ribeiro, A. J. M.; Ramos, M. J.; Fernandes, P. A.; Toscano, M.; Russo, N.. "New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models". Archives of Biochemistry and Biophysics 582 (2015): 107-115. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000360781200012&KeyUID=WOS:000360781200012.
    10.1016/j.abb.2015.03.002
  132. Cerqueira, Nuno M. F. S. A.; Gonzalez, Pablo J.; Fernandes, Pedro A.; Moura, Jose J. G.; Ramos, Maria Joao. "Periplasmic Nitrate Reductase and Formate Dehydrogenase: Similar Molecular Architectures with Very Different Enzymatic Activities". Accounts of Chemical Research 48 11 (2015): 2875-2884. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000365150500009&KeyUID=WOS:000365150500009.
    10.1021/acs.accounts.5b00333
  133. Moorthy, Nshn; Cerqueira, Nmfsa; Ramos, M. J.; Fernandes, P. A.. "Ligand based analysis on HMG-CoA reductase inhibitors". Chemometrics and Intelligent Laboratory Systems 140 (2015): 102-116. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000349062500011&KeyUID=WOS:000349062500011.
    10.1016/j.chemolab.2014.11.009
  134. Ribeiro, A. J. M.; Yang, L. F.; Ramos, M. J.; Fernandes, P. A.; Liang, Z. X.; Hirao, H.. "Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase". Acs Catalysis 5 6 (2015): 3740-3751. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000355964300062&KeyUID=WOS:000355964300062.
    10.1021/acscatal.5b00528
  135. Cerqueira, Nmfsa; Coelho, C.; Bras, N. F.; Fernandes, P. A.; Garattini, E.; Terao, M.; Romao, M. J.; Ramos, M. J.. "Insights into the structural determinants of substrate specificity and activity in mouse aldehyde oxidases". Journal of Biological Inorganic Chemistry 20 2 (2015): 209-217. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000350236100004&KeyUID=WOS:000350236100004.
    10.1007/s00775-014-1198-2
  136. Ribeiro, A. J. M.; Santos-Martins, D.; Russo, N.; Rarnos, M. J.; Fernandes, P. A.. "Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease". Acs Catalysis 5 9 (2015): 5617-5626. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000361089700073&KeyUID=WOS:000361089700073.
    10.1021/acscatal.5b00759
  137. Pinto, G. P.; Bras, N. F.; Perez, M. A. S.; Fernandes, P. A.; Russo, N.; Ramos, M. J.; Toscano, M.. "Establishing the Catalytic Mechanism of Human Pancreatic alpha-Amylase with QM/MM Methods". Journal of Chemical Theory and Computation 11 6 (2015): 2508-2516. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000356201700012&KeyUID=WOS:000356201700012.
    10.1021/acs.jctc.5b00222
  138. Moreira, I. S.; Martins, J. M.; Coimbra, J. T. S.; Ramos, M. J.; Fernandes, P. A.. "A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy". Physical Chemistry Chemical Physics 17 4 (2015): 2378-2387. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000346906700012&KeyUID=WOS:000346906700012.
    10.1039/c4cp04688a
  139. Moorthy, NSHN; Bras, NF; Ramos, MJ; Fernandes, PA. "Binding mode prediction and identification of new lead compounds from natural products as renin and angiotensin converting enzyme inhibitors". RSC ADVANCES (2014): https://www.authenticus.pt/P-009-DFG.
    10.1039/c4ra00856a
  140. Bidarian Moniri, A; Ramos, MJ; Ejnell, H. "Autoinflation for treatment of persistent otitis media with effusion in children: A cross-over study with a 12-month follow-up". INTERNATIONAL JOURNAL OF PEDIATRIC OTORHINOLARYNGOLOGY (2014):
    10.1016/j.ijporl.2014.05.015
  141. Coimbra, J.T.S.; Sousa, S.F.; Fernandes, P.A.; Rangel, M.; Ramos, M.J.. "Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble". Journal of Biomolecular Structure and Dynamics 32 1 (2014): 88-103. http://www.scopus.com/inward/record.url?eid=2-s2.0-84889680410&partnerID=MN8TOARS.
    10.1080/07391102.2012.750250
  142. Silva, A. M. N.; Sousa, P. R. H.; Coimbra, J. T. S.; Bras, N. F.; Vitorino, R.; Fernandes, P. A.; Ramos, M. J.; Rangel, M.; Domingues, P.. "The glycation site specificity of human serum transferrin is a determinant for transferrin's functional impairment under elevated glycaemic conditions". Biochemical Journal 461 (2014): 33-42. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000337770800003&KeyUID=WOS:000337770800003.
    10.1042/bj20140133
  143. Fernandes, A.; Ivanova, G.; Bras, N. F.; Mateus, N.; Ramos, M. J.; Rangel, M.; de Freitas, V.. "Structural characterization of inclusion complexes between cyanidin-3-0-glucoside and beta-cyclodextrin". Carbohydrate Polymers 102 (2014): 269-277. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000331779600035&KeyUID=WOS:000331779600035.
    10.1016/j.carbpol.2013.11.037
  144. Aranda, J.; Cerqueira, Nmfsa; Fernandes, P. A.; Roca, M.; Tunon, I.; Ramos, M. J.. "The Catalytic Mechanism of Carboxylesterases: A Computational Study". Biochemistry 53 36 (2014): 5820-5829. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000341801000012&KeyUID=WOS:000341801000012.
    10.1021/bi500934j
  145. Coimbra, J. T. S.; Moniz, T.; Bras, N. F.; Iyanova, G.; Fernandes, P. A.; Ramos, M. J.; Rangel, M.. "Relevant Interactions of Antimicrobial Iron Chelators and Membrane Models Revealed by Nuclear Magnetic Resonance and Molecular Dynamics Simulations". Journal of Physical Chemistry B 118 50 (2014): 14590-14601. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000346759400004&KeyUID=WOS:000346759400004.
    10.1021/jp509491p
  146. Marcial, B. L.; Sousa, S. F.; Dos Santos, H. F.; Ramos, M. J.. "Structural and dynamics analysis of matrix metalloproteinases MMP-2 complexed with chemically modified tetracyclines (CMTs)". Journal of Biomolecular Structure & Dynamics 32 12 (2014): 1907-1918. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340447600002&KeyUID=WOS:000340447600002.
    10.1080/07391102.2013.842186
  147. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "QM/MM Study and MD Simulations on the Hypertension Regulator Angiotensin-Converting Enzyme". Acs Catalysis 4 8 (2014): 2587-2597. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000339983800021&KeyUID=WOS:000339983800021.
    10.1021/cs500093h
  148. Calixto, A. R.; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Reaction Mechanism of Human Renin Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations". Acs Catalysis 4 11 (2014): 3869-3876. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344639300008&KeyUID=WOS:000344639300008.
    10.1021/cs500497f
  149. Martins, S. A.; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field". Journal of Chemical Theory and Computation 10 8 (2014): 3570-3577. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340351200067&KeyUID=WOS:000340351200067.
    10.1021/ct500346y
  150. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Predictive QSAR models development and validation for human ether-a-go-go related gene (hERG) blockers using newer tools". Journal of Enzyme Inhibition and Medicinal Chemistry 29 3 (2014): 317-324. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000336311600003&KeyUID=WOS:000336311600003.
    10.3109/14756366.2013.779264
  151. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Molecular dynamics studies on both bound and unbound renin protease". Journal of Biomolecular Structure & Dynamics 32 3 (2014): 351-363. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000329823600002&KeyUID=WOS:000329823600002.
    10.1080/07391102.2013.768553
  152. Ngo, H. P. T.; Cerqueira, Nmfsa; Kim, J. K.; Hong, M. K.; Fernandes, P. A.; Ramos, M. J.; Kang, L. W.. "PLP undergoes conformational changes during the course of an enzymatic reaction". Acta Crystallographica Section D-Biological Crystallography 70 (2014): 596-606. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000331554500038&KeyUID=WOS:000331554500038.
    10.1107/s1399004713031283
  153. Coimbra, J. T. S.; Neves, R. P. P.; Passos, O.; Jarukanont, D.; Fernandes, P. A.; Patel, S.; Garcia, M. E.; Ramos, M. J.. "Influence of the environment on protein bond energies". Chemical Physics Letters 615 (2014): 75-82. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344747400014&KeyUID=WOS:000344747400014.
    10.1016/j.cplett.2014.09.066
  154. Dourado, Dfar; Fernandes, P. A.; Mannervik, B.; Ramos, M. J.. "Isomerization of Delta(5)-Androstene-3,17-dione into Delta(4)-Androstene-3, 17-dione Catalyzed by Human Glutathione Transferase A3-3: A Computational Study Identifies a Dual Role for Glutathione". Journal of Physical Chemistry A 118 31 (2014): 5790-5800. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340222500008&KeyUID=WOS:000340222500008.
    10.1021/jp410810q
  155. Moorthy, Nshn; Pratheepa, V.; Ramos, M. J.; Vasconcelos, V.; Fernandes, P. A.. "Fused Aryl-Phenazines: Scaffold for the Development of Bioactive Molecules". Current Drug Targets 15 7 (2014): 681-688. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000337168100003&KeyUID=WOS:000337168100003.
    10.2174/1389450115666140205152007
  156. Bras, N. F.; Cerqueira, Nmfsa; Ramos, M. J.; Fernandes, P. A.. "Glycosidase inhibitors: a patent review (2008-2013)". Expert Opinion on Therapeutic Patents 24 8 (2014): 857-874. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340430700003&KeyUID=WOS:000340430700003.
    10.1517/13543776.2014.916280
  157. Hong, M. K.; Ribeiro, A. J. M.; Kim, J. K.; Ngo, H. P. T.; Kim, J.; Lee, C. H.; Ahn, Y. J.; et al. "Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli". Acta Crystallographica Section D-Biological Crystallography 70 (2014): 1297-1310. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000335952500012&KeyUID=WOS:000335952500012.
    10.1107/s1399004714002570
  158. Sousa, S. F.; Cerqueira, Nmfsa; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Enzymatic "Tricks": Carboxylate Shift and Sulfur Shift". International Journal of Quantum Chemistry 114 19 (2014): 1253-1256. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000341718400003&KeyUID=WOS:000341718400003.
    10.1002/qua.24689
  159. Gesto, D. S.; Cerqueira, Nmfsa; Ramos, M. J.; Fernandes, P. A.. "Discovery of new druggable sites in the anti-cholesterol target HMG-CoA reductase by computational alanine scanning mutagenesis". Journal of Molecular Modeling 20 4 (2014): 13-13. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000334934900044&KeyUID=WOS:000334934900044.
    10.1007/s00894-014-2178-8
  160. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Discovery of New Sites for Drug Binding to the Hypertension-Related Renin-Angiotensinogen Complex". Chemical Biology & Drug Design 83 4 (2014): 427-439. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000332886400006&KeyUID=WOS:000332886400006.
    10.1111/cbdd.12258
  161. Ribeiro, J. V.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "chem-path-tracker: An Automated Tool to Analyze Chemical Motifs in Molecular Structures". Chemical Biology & Drug Design 84 1 (2014): 44-53. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000337665900004&KeyUID=WOS:000337665900004.
    10.1111/cbdd.12349
  162. Moorthy, Nshn; Martins, S. A.; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Classification study of solvation free energies of organic molecules using machine learning techniques". Rsc Advances 4 106 (2014): 61624-61630. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000345656600051&KeyUID=WOS:000345656600051.
    10.1039/c4ra07961b
  163. Araujo, A. R.; Ribeiro, A. J. M.; Fernandes, P. A.; Ramos, M. J.. "Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations". Journal of Chemical Theory and Computation 10 12 (2014): 5458-5466. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000346324000026&KeyUID=WOS:000346324000026.
    10.1021/ct500570g
  164. Jarukanont, D.; Coimbra, J. T. S.; Bauerhenne, B.; Fernandes, P. A.; Patel, S.; Ramos, M. J.; Garcia, M. E.. "Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase". Physical Chemistry Chemical Physics 16 39 (2014): 21768-21777. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000343072900083&KeyUID=WOS:000343072900083.
    10.1039/c4cp02289k
  165. Santos-Martins, D.; Forli, S.; Ramos, M. J.; Olson, A. J.. "AutoDock4(Zn): An Improved Auto Dock Force Field for Small-Molecule Docking to Zinc Metalloproteins". Journal of Chemical Information and Modeling 54 8 (2014): 2371-2379. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340861900018&KeyUID=WOS:000340861900018.
    10.1021/ci500209e
  166. Neves, R. P. P.; Fernandes, P. A.; Varandas, A. J. C.; Ramos, M. J.. "Benchmarking of Density Functionals for the Accurate Description of Thiol-Disulfide Exchange". Journal of Chemical Theory and Computation 10 11 (2014): 4842-4856. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344905300010&KeyUID=WOS:000344905300010.
    10.1021/ct500840f
  167. Bras, N. F.; Ribeiro, A. J. M.; Oliveira, M.; Paixao, N. M.; Tamames, J. A.; Fernandes, P. A.; Ramos, M. J.. "Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns". Journal of Molecular Modeling 20 6 (2014): 14-14. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000338632200028&KeyUID=WOS:000338632200028.
    10.1007/s00894-014-2271-z
  168. Moorthy, NSHN; Sousa, SF; Ramos, MJ; Fernandes, PA. "Farnesyltransferase Inhibitors: A Comprehensive Review Based on Quantitative Structural Analysis". CURRENT MEDICINAL CHEMISTRY (2013): https://www.authenticus.pt/P-006-JES.
    10.2174/09298673113206660262
  169. Bidarian Moniri, A; Ramos, MJ; Goncalves, I; Ejnell, H. "A new device for treatment of persistent otitis media with effusion". International Journal of Pediatric Otorhinolaryngology (2013):
    10.1016/j.ijporl.2013.10.009
  170. Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "QSAR and pharmacophore analysis of a series of piperidinyl urea derivatives as hERG blockers and H3 antagonists". Current Drug Discovery Technologies 10 1 (2013): 47-58. http://www.scopus.com/inward/record.url?eid=2-s2.0-84875452236&partnerID=MN8TOARS.
  171. Oliveira, B. L.; Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.; Santos, I.; Correia, J. D. G.. "Theoretical studies on the binding of rhenium(I) complexes to inducible nitric oxide synthase". Journal of Molecular Graphics & Modelling 45 (2013): 13-25. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000326849200002&KeyUID=WOS:000326849200002.
    10.1016/j.jmgm.2013.07.007
  172. Moreira, I. S.; Martins, J. M.; Ramos, R. M.; Fernandes, P. A.; Ramos, M. J.. "Understanding the importance of the aromatic amino-acid residues as hot-spots". Biochimica Et Biophysica Acta-Proteins and Proteomics 1834 1 (2013): 404-414. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000314620400042&KeyUID=WOS:000314620400042.
    10.1016/j.bbapap.2012.07.005
  173. Cerqueira, Nmfsa; Fernandes, P. A.; Gonzalez, P. J.; Moura, J. J. G.; Ramos, M. J.. "The Sulfur Shift: An Activation Mechanism for Periplasmic Nitrate Reductase and Formate Dehydrogenase". Inorganic Chemistry 52 19 (2013): 10766-10772. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000326319800017&KeyUID=WOS:000326319800017.
    10.1021/ic3028034
  174. Teixeira, N.; Cruz, L.; Bras, N. F.; Mateus, N.; Ramos, M. J.; de Freitas, V.. "Structural Features of Copigmentation of Oenin with Different Polyphenol Copigments". Journal of Agricultural and Food Chemistry 61 28 (2013): 6942-6948. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000322103600022&KeyUID=WOS:000322103600022.
    10.1021/jf401174b
  175. Ornellas, F. R.; Ramos, M. J.. "Preface". Theoretical Chemistry Accounts 132 3 (2013): 5-5. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000318295200002&KeyUID=WOS:000318295200002.
    10.1007/s00214-012-1319-3
  176. Sousa, S. F.; Ribeiro, A. J. M.; Coimbra, J. T. S.; Neves, R. P. P.; Martins, S. A.; Moorthy, Nshn; Fernandes, P. A.; Ramos, M. J.. "Protein-Ligand Docking in the New Millennium - A Retrospective of 10 Years in the Field". Current Medicinal Chemistry 20 18 (2013): 2296-2314. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000318486200002&KeyUID=WOS:000318486200002.
    10.2174/0929867311320180002
  177. Carvalho, A. T. P.; Teixeira, A. F. S.; Ramos, M. J.; Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Parameters for molecular dynamics simulations of iron-sulfur proteins". Journal of Computational Chemistry 34 18 (2013): 1540-1548. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000320177700003&KeyUID=WOS:000320177700003.
    10.1002/jcc.23287
  178. Silva, P. J.; Perez, M. A. S.; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Improving the study of proton transfers between amino acid side chains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls (vol 131, pg 1179, 2012)". Theoretical Chemistry Accounts 132 2 (2013): 1-1. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000318294700003&KeyUID=WOS:000318294700003.
    10.1007/s00214-012-1307-7
  179. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Human Ether-a-Go-Go-Related Gene Channel Blockers and its Structural Analysis for Drug Design". Current Drug Targets 14 1 (2013): 102-113. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000316871200011&KeyUID=WOS:000316871200011.
  180. Gesto, D. S.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Unraveling the Enigmatic Mechanism of L-Asparaginase II with QM/QM Calculations". Journal of the American Chemical Society 135 19 (2013): 7146-7158. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000319250200017&KeyUID=WOS:000319250200017.
    10.1021/ja310165u
  181. Moorthy, Nshn; Cerqueira, Nmfsa; Ramos, M. J.; Fernandes, P. A.. "Combined ligand and structure based binding mode analysis of oxidosqualene cyclase inhibitors". Rsc Advances 3 45 (2013): 23409-23422. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000326395800097&KeyUID=WOS:000326395800097.
    10.1039/c3ra43670e
  182. Moreira, I. S.; Martins, J. M.; Ramos, R. M.; Fernandes, P. A.; Ramos, M. J.; Moreira, I.S.; Ramos, R.M.; et al. "Are Hot-Spots Occluded from Water?". Biophysical Journal 104 2 (2013): 505A-505A. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000316074305069&KeyUID=WOS:000316074305069.
    10.1080/07391102.2012.758598
  183. Ribeiro, A. J. M.; Ramos, M. J.; Fernandes, P. A.; Russo, N.. "A DFT study of the applicability of the charge balance model in two-metal enzymes: The case of cAMP-dependent protein kinase". Chemical Physics Letters 571 (2013): 66-70. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000319109900011&KeyUID=WOS:000319109900011.
    10.1016/j.cplett.2013.03.085
  184. Ribeiro, A.J.; Alberto, M.E.; Ramos, M.J.; Fernandes, P.A.; Russo, N.. "The catalytic mechanism of protein phosphatase 5 established by DFT calculations". Chemistry (Weinheim an der Bergstrasse, Germany) 19 42 (2013): 14081-14089. http://www.scopus.com/inward/record.url?eid=2-s2.0-84928700256&partnerID=MN8TOARS.
    10.1002/chem.201301565
  185. Ribeiro, J.V.; Tamames, J.A.C.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Volarea - A bioinformatics tool to calculate the surface area and the volume of molecular systems". Chemical Biology and Drug Design 82 6 (2013): 743-755. http://www.scopus.com/inward/record.url?eid=2-s2.0-84889887906&partnerID=MN8TOARS.
    10.1111/cbdd.12197
  186. Moorthy, N.S.H.N.; Cerqueira, N.M.F.S.A.; Ramos, M.J.; Fernandes, P.A.. "Aryl-and heteroaryl-thiosemicarbazone derivatives and their metal complexes: A pharmacological template". Recent Patents on Anti-Cancer Drug Discovery 8 2 (2013): 168-182. http://www.scopus.com/inward/record.url?eid=2-s2.0-84875300425&partnerID=MN8TOARS.
    10.2174/157489213805290583
  187. Martins, S.A.; Perez, M.A.S.; Moreira, I.S.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "Computational alanine scanning mutagenesis: MM-PBSA vs TI". Journal of Chemical Theory and Computation 9 3 (2013): 1311-1319. http://www.scopus.com/inward/record.url?eid=2-s2.0-84874848450&partnerID=MN8TOARS.
    10.1021/ct4000372
  188. Oliveira, B.L.; Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.; Santos, I.; Correia, J.D.G.. "Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms". Journal of Molecular Modeling 19 4 (2013): 1537-1551. http://www.scopus.com/inward/record.url?eid=2-s2.0-84876407327&partnerID=MN8TOARS.
    10.1007/s00894-012-1677-8
  189. Sousa, S.F.; Coimbra, J.T.S.; Paramos, D.; Pinto, R.; Guimarães, R.S.; Teixeira, V.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif". Journal of Molecular Modeling 19 2 (2013): 673-688. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877128216&partnerID=MN8TOARS.
    10.1007/s00894-012-1590-1
  190. Dourado, D.F.A.R.; Fernandes, P.A.; Ramos, M.J.; Mannervik, B.. "Mechanism of glutathione transferase P1-1-catalyzed activation of the prodrug canfosfamide (TLK286, TELCYTA)". Biochemistry 52 45 (2013): 8069-8078. http://www.scopus.com/inward/record.url?eid=2-s2.0-84887597240&partnerID=MN8TOARS.
    10.1021/bi4005705
  191. Oliveira, J.; Da Silva, M.A.; Parola, A.J.; Mateus, N.; Brás, N.F.; Ramos, M.J.; De Freitas, V.. "Structural characterization of a A-type linked trimeric anthocyanin derived pigment occurring in a young Port wine". Food Chemistry 141 3 (2013): 1987-1996. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879047061&partnerID=MN8TOARS.
    10.1016/j.foodchem.2013.04.091
  192. Gesto, D.S.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Gemcitabine: A critical nucleoside for cancer therapy". Current Medicinal Chemistry 19 7 (2012): 1076-1087. http://www.scopus.com/inward/record.url?eid=2-s2.0-84858173640&partnerID=MN8TOARS.
    10.2174/092986712799320682
  193. Moorthy, Nshn; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "In silico Based Structural Analysis of Some Piperidine Analogs as Farnesyltransferase Inhibitors". Medicinal Chemistry 8 5 (2012): 853-864. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000309650400011&KeyUID=WOS:000309650400011.
    10.2174/157340612802084171
  194. Moorthy, Nshn; Bras, N. F.; Ramos, M. J.; Fernandes, P. A.. "Virtual screening and QSAR study of some pyrrolidine derivatives as alpha-mannosidase inhibitors for binding feature analysis". Bioorganic & Medicinal Chemistry 20 24 (2012): 6945-6959. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000311421300006&KeyUID=WOS:000311421300006.
    10.1016/j.bmc.2012.10.011
  195. De Rienzo, F.; Barbosa, A. J. M.; Perez, M. A. S.; Fernandes, P. A.; Ramos, M. J.; Menziani, M. C.. "The extracellular subunit interface of the 5-HT3 receptors: a computational alanine scanning mutagenesis study". Journal of Biomolecular Structure & Dynamics 30 3 (2012): 280-298. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000306119000004&KeyUID=WOS:000306119000004.
    10.1080/07391102.2012.680029
  196. Bras, N. F.; Ramos, M. J.; Fernandes, P. A.. "The catalytic mechanism of mouse renin studied with QM/MM calculations". Physical Chemistry Chemical Physics 14 36 (2012): 12605-12613. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000307900800020&KeyUID=WOS:000307900800020.
    10.1039/c2cp41422h
  197. Moorthy, Nshn; Cerqueira, N. S.; Ramos, M. J.; Fernandes, P. A.. "QSAR analysis of 2-benzoxazolyl hydrazone derivatives for anticancer activity and its possible target prediction". Medicinal Chemistry Research 21 2 (2012): 133-144. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000298882100001&KeyUID=WOS:000298882100001.
    10.1007/s00044-010-9510-3
  198. Nave, F.; Bras, N. F.; Cruz, L.; Teixeira, N.; Mateus, N.; Ramos, M. J.; Di Meo, F.; et al. "Influence of a Flavan-3-ol Substituent on the Affinity of Anthocyanins (Pigments) toward Vinylcatechin Dimers and Proanthocyanidins (Copigments)". Journal of Physical Chemistry B 116 48 (2012): 14089-14099. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000311921700017&KeyUID=WOS:000311921700017.
    10.1021/jp307782y
  199. Ribeiro, J. V.; Cerqueira, Nmfsa; Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "CompASM: an Amber-VMD alanine scanning mutagenesis plug-in". Theoretical Chemistry Accounts 131 10 (2012): 7-7. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000309862600005&KeyUID=WOS:000309862600005.
    10.1007/s00214-012-1271-2
  200. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Computational enzymatic catalysis - clarifying enzymatic mechanisms with the help of computers". Physical Chemistry Chemical Physics 14 36 (2012): 12431-12441. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000307900800003&KeyUID=WOS:000307900800003.
    10.1039/c2cp41180f
  201. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Comparative Structural Analysis of a-Glucosidase Inhibitors on Difference Species: A Computational Study". Archiv Der Pharmazie 345 4 (2012): 265-274. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000302607300003&KeyUID=WOS:000302607300003.
    10.1002/ardp.201100047
  202. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Analysis of van der Waals surface area properties for human ether-a-go-go-related gene blocking activity: computational study on structurally diverse compounds". Sar and Qsar in Environmental Research 23 5-6 (2012): 521-536. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000306712600008&KeyUID=WOS:000306712600008.
    10.1080/1062936x.2012.666264
  203. Coelho, C.; Mahro, M.; Trincão, J.; Carvalho, A.T.P.; Ramos, M.J.; Terao, M.; Garattini, E.; Leimkühler, S.; Romão, M.J.. "The first mammalian aldehyde oxidase crystal structure: Insights into substrate specificity". Journal of Biological Chemistry 287 48 (2012): 40690-40702. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870012251&partnerID=MN8TOARS.
    10.1074/jbc.m112.390419
  204. Marcial, B.L.; Sousa, S.F.; Barbosa, I.L.; Dos Santos, H.F.; Ramos, M.J.. "Chemically modified tetracyclines as inhibitors of MMP-2 matrix metalloproteinase: A molecular and structural study". Journal of Physical Chemistry B 116 46 (2012): 13644-13654. http://www.scopus.com/inward/record.url?eid=2-s2.0-84869994239&partnerID=MN8TOARS.
    10.1021/jp3079748
  205. Zhang, W.; Dourado, D.F.A.R.; Fernandes, P.A.; Ramos, M.J.; Mannervik, B.. "Multidimensional epistasis and fitness landscapes in enzyme evolution". Biochemical Journal 445 1 (2012): 39-46. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862489556&partnerID=MN8TOARS.
    10.1042/bj20120136
  206. Moorthy, N.S.H.N.; Cerqueira, N.M.F.S.A.; Ramos, M.J.; Fernandes, P.A.. "QSAR and pharmacophore analysis of thiosemicarbazone derivatives as ribonucleotide reductase inhibitors". Medicinal Chemistry Research 21 6 (2012): 739-746. http://www.scopus.com/inward/record.url?eid=2-s2.0-84861897147&partnerID=MN8TOARS.
    10.1007/s00044-011-9580-x
  207. Narayana Moorthy, N.S.H.; Ramos, M.J.; Fernandes, P.A.. "Structural analysis of structurally diverse a-glucosidase inhibitors for active site feature analysis". Journal of Enzyme Inhibition and Medicinal Chemistry 27 5 (2012): 649-657. http://www.scopus.com/inward/record.url?eid=2-s2.0-84866120433&partnerID=MN8TOARS.
    10.3109/14756366.2011.605359
  208. Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Structural analysis of 2-piperidin-4-yl-actamide derivatives for hERG blocking and MCH R1 antagonistic activities". Current Drug Discovery Technologies 9 1 (2012): 25-38. http://www.scopus.com/inward/record.url?eid=2-s2.0-84858269405&partnerID=MN8TOARS.
    10.2174/157016312799304543
  209. Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.. "The catalytic mechanism of HIV-1 integrase for DNA 3'-end processing established by QM/MM calculations". Journal of the American Chemical Society 134 32 (2012): 13436-13447. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865142881&partnerID=MN8TOARS.
    10.1021/ja304601k
  210. Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Studies on a-glucosidase inhibitors development: Magic molecules for the treatment of carbohydrate mediated diseases". Mini-Reviews in Medicinal Chemistry 12 8 (2012): 713-720. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862625361&partnerID=MN8TOARS.
    10.2174/138955712801264837
  211. Silva, P.J.; Ramos, M.J.. "Computational characterization of the substrate-binding mode in coproporphyrinogen III oxidase". Journal of Physical Chemistry B 115 8 (2011): 1903-1910. http://www.scopus.com/inward/record.url?eid=2-s2.0-79951992419&partnerID=MN8TOARS.
    10.1021/jp110289d
  212. Cerqueira, Nmfsa; Ribeiro, J.; Fernandes, P. A.; Ramos, M. J.. "vsLab-An Implementation for Virtual High-Throughput Screening Using AutoDock and VMD". International Journal of Quantum Chemistry 111 6 (2011): 1208-1212. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000288096500009&KeyUID=WOS:000288096500009.
    10.1002/qua.22738
  213. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "The Catalytic Mechanism of RNA Polymerase II". Journal of Chemical Theory and Computation 7 4 (2011): 1177-1188. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000289315700039&KeyUID=WOS:000289315700039.
    10.1021/ct100579w
  214. Passos, O.; Fernandes, P. A.; Ramos, M. J.. "Theoretical insights into the catalytic mechanism of beta-hexosaminidase". Theoretical Chemistry Accounts 129 1 (2011): 119-129. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000289484000012&KeyUID=WOS:000289484000012.
    10.1007/s00214-011-0904-1
  215. Silva, P. J.; Ramos, M. J.. "Successes and failures of DFT functionals in acid/base and redox reactions of organic and biochemical interest". Computational and Theoretical Chemistry 966 1-3 (2011): 120-126. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000291325100018&KeyUID=WOS:000291325100018.
    10.1016/j.comptc.2011.02.022
  216. Neves, A. R.; Fernandes, P. A.; Ramos, M. J.. "The Accuracy of Density Functional Theory in the Description of Cation-pi and pi-Hydrogen Bond Interactions". Journal of Chemical Theory and Computation 7 7 (2011): 2059-2067. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000292617900007&KeyUID=WOS:000292617900007.
    10.1021/ct2001667
  217. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Structural analysis of alpha-glucosidase inhibitors by validated QSAR models using topological and hydrophobicity based descriptors". Chemometrics and Intelligent Laboratory Systems 109 2 (2011): 101-112. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000297392800001&KeyUID=WOS:000297392800001.
    10.1016/j.chemolab.2011.02.010
  218. Moorthy, Nshn; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors". Journal of Enzyme Inhibition and Medicinal Chemistry 26 6 (2011): 777-791. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000297057900003&KeyUID=WOS:000297057900003.
    10.3109/14756366.2011.552885
  219. Passos, O.; Fernandes, P. A.; Ramos, M. J.. "QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human beta-HexosaminidaseA". Journal of Physical Chemistry B 115 49 (2011): 14751-14759. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000297608600046&KeyUID=WOS:000297608600046.
    10.1021/jp205826n
  220. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.; Hari Narayana Moorthy, N.S.; Ramos, M.J.; Fernandes, P.A.. "QSAR Analysis of Isosteviol Derivatives as alpha-Glucosidase Inhibitors with Element Count and Other Descriptors". Letters in Drug Design & Discovery 8 1 (2011): 14-25. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000285781700003&KeyUID=WOS:000285781700003.
    10.2174/157018011793663859
  221. Tamames, J. A. C.; Ramos, M. J.. "Metals in proteins: cluster analysis studies". Journal of Molecular Modeling 17 3 (2011): 429-442. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000289531200003&KeyUID=WOS:000289531200003.
    10.1007/s00894-010-0733-5
  222. Oliveira, E. F.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Mechanism of Formation of the Internal Aldimine in Pyridoxal 5 '-Phosphate-Dependent Enzymes". Journal of the American Chemical Society 133 39 (2011): 15496-15505. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000295911500052&KeyUID=WOS:000295911500052.
    10.1021/ja204229m
  223. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "hERG binding feature analysis of structurally diverse compounds by QSAR and fragmental analysis". Rsc Advances 1 6 (2011): 1126-1136. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000295920900030&KeyUID=WOS:000295920900030.
    10.1039/c1ra00131k
  224. Bras, N. F.; Cruz, L.; Fernandes, P. A.; De Freitas, V.; Ramos, M. J.. "Conformational Study of Two Diasteroisomers of Vinylcatechin Dimers in a Methanol Solution". International Journal of Quantum Chemistry 111 7-8 (2011): 1498-1510. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000288873300029&KeyUID=WOS:000288873300029.
    10.1002/qua.22631
  225. Sousa, S. F.; Tamames, B.; Fernandes, P. A.; Ramos, M. J.. "Detailed Atomistic Analysis of the HIV-1 Protease Interface". Journal of Physical Chemistry B 115 21 (2011): 7045-7057. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000290914600027&KeyUID=WOS:000290914600027.
    10.1021/jp200075s
  226. Silva, P. J.; Ramos, M. J.. "Computational Insights Into the Photochemical Step of the Reaction Catalyzed by Protochlorophylide Oxidoreductase". International Journal of Quantum Chemistry 111 7-8 (2011): 1472-1479. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000288873300026&KeyUID=WOS:000288873300026.
    10.1002/qua.22671
  227. Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Computational Mechanistic Studies Addressed to the Transimination Reaction Present in All Pyridoxal 5 '-Phosphate-Requiring Enzymes". Journal of Chemical Theory and Computation 7 5 (2011): 1356-1368. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000290293000014&KeyUID=WOS:000290293000014.
    10.1021/ct1002219
  228. Oliveira, J.; Petrov, V.; Parola, A. J.; Pina, F.; Azevedo, J.; Teixeira, N.; Bras, N. F.; et al. "Chemical Behavior of Methylpyranomalvidin-3-O-glucoside in Aqueous Solution Studied by NMR and UV-Visible Spectroscopy". Journal of Physical Chemistry B 115 6 (2011): 1538-1545. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000287066600024&KeyUID=WOS:000287066600024.
    10.1021/jp110593c
  229. Bras, N. F.; Perez, M. A. S.; Fernandes, P. A.; Silva, P. J.; Ramos, M. J.. "Accuracy of Density Functionals in the Prediction of Electronic Proton Affinities of Amino Acid Side Chains". Journal of Chemical Theory and Computation 7 12 (2011): 3898-3908. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000298118000006&KeyUID=WOS:000298118000006.
    10.1021/ct200309v
  230. Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Analysis of the a-glucosidase inhibitory activity of chromenone derivatives based on their molecular features: A computational study". Medicinal Chemistry 7 6 (2011): 526-533. http://www.scopus.com/inward/record.url?eid=2-s2.0-80755125976&partnerID=MN8TOARS.
  231. Perez, M.A.S.; Sousa, S.F.; Oliveira, E.F.T.; Fernandes, P.A.; Ramos, M.J.. "Detection of farnesyltransferase interface hot spots through computational alanine scanning mutagenesis". Journal of Physical Chemistry B 115 51 (2011): 15339-15354. http://www.scopus.com/inward/record.url?eid=2-s2.0-84255176172&partnerID=MN8TOARS.
    10.1021/jp205481y
  232. Narayana Moorthy, N.S.H.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "In silico-based structural analysis of arylthiophene derivatives for FTase inhibitory activity, hERG, and other toxic effects". Journal of Biomolecular Screening 16 9 (2011): 1037-1046. http://www.scopus.com/inward/record.url?eid=2-s2.0-80053498208&partnerID=MN8TOARS.
    10.1177/1087057111414899
  233. Narayana Moorthy, N.S.H.; Ramos, M.J.; Fernandes, P.A.. "Prediction of the relationship between the structural features of andrographolide derivatives and aî±-glucosidase inhibitory activity: A quantitative structure-activity relationship (QSAR) Study". Journal of Enzyme Inhibition and Medicinal Chemistry 26 1 (2011): 78-87. http://www.scopus.com/inward/record.url?eid=2-s2.0-79851474038&partnerID=MN8TOARS.
    10.3109/14756361003724760
  234. Hari Narayana Moorthy, N.S.; Ramos, M.J.; Fernandes, P.A.; Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Topological, hydrophobicity, and other descriptors on a-glucosidase inhibition: A QSAR study on xanthone derivatives". Journal of Enzyme Inhibition and Medicinal Chemistry 26 6 (2011): 755-766. http://www.scopus.com/inward/record.url?eid=2-s2.0-81355149312&partnerID=MN8TOARS.
    10.3109/14756366.2010.549089
  235. Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Protein-protein docking dealing with the unknown". Journal of Computational Chemistry 31 2 (2010): 317-342. http://www.scopus.com/inward/record.url?eid=2-s2.0-76149086786&partnerID=MN8TOARS.
    10.1002/jcc.21276
  236. Perez, M.A.S.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Ribonucleotide reductase: A mechanistic portrait of substrate analogues inhibitors". Current Medicinal Chemistry 17 26 (2010): 2854-2872. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955606286&partnerID=MN8TOARS.
    10.2174/092986710792065054
  237. Marques, A.T.; Fernandes, P.A.; Ramos, M.J.. "Structural analysis of ABAD point mutations causing 2-methyl-3- hydroxylbutyryl-coA deficiency". International Journal of Quantum Chemistry 110 1 (2010): 148-160. http://www.scopus.com/inward/record.url?eid=2-s2.0-73849124964&partnerID=MN8TOARS.
    10.1002/qua.22091
  238. Silva, P.J.; Schulz, C.; Jahn, D.; Jahn, M.; Ramos, M.J.. "A tale of two acids: When arginine is a more appropriate acid than H 3O+". Journal of Physical Chemistry B 114 27 (2010): 8994-9001. http://www.scopus.com/inward/record.url?eid=2-s2.0-77954470518&partnerID=MN8TOARS.
    10.1021/jp100961s
  239. Alberto, M.E.; Marino, T.; Ramos, M.J.; Russo, N.. "Atomistic details of the catalytic mechanism of Fe(III)-Zn(II) purple acid phosphatase". Journal of Chemical Theory and Computation 6 8 (2010): 2424-2433. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955583791&partnerID=MN8TOARS.
    10.1021/ct100187c
  240. Brás, N.F.; Ramos, M.J.; Fernandes, P.A.. "DFT studies on the ß-glycosidase catalytic mechanism: The deglycosylation step". Journal of Molecular Structure: THEOCHEM 946 1-3 (2010): 125-133. http://www.scopus.com/inward/record.url?eid=2-s2.0-77649190284&partnerID=MN8TOARS.
    10.1016/j.theochem.2009.08.039
  241. Dourado, D.F.A.R.; Fernandes, P.A.; Mannervik, B.; Ramos, M.J.. "Glutathione transferase A1-1: Catalytic importance of arginine 15". Journal of Physical Chemistry B 114 4 (2010): 1690-1697. http://www.scopus.com/inward/record.url?eid=2-s2.0-75749092981&partnerID=MN8TOARS.
    10.1021/jp908251z
  242. Perez, M. A. S.; Fernandes, P. A.; Ramos, M. J.. "Understanding the Mechanism for Ribonucleotide Reductase Inactivation by 2 '-Deoxy-2 '-methylenecytidine-5 '-diphosphate". Journal of Chemical Theory and Computation 6 9 (2010): 2770-2781.
    10.1021/ct1002175
  243. Perez, M. A. S.; Fernandes, P. A.; Ramos, M. J.. "Substrate Recognition in HIV-1 Protease: A Computational Study". Journal of Physical Chemistry B 114 7 (2010): 2525-2532.
    10.1021/jp910958u
  244. Bras, N. F.; Goncalves, R.; Fernandes, P. A.; Mateus, N.; Ramos, M. J.; de Freitas, V.. "Understanding the Binding of Procyanidins to Pancreatic Elastase by Experimental and Computational Methods". Biochemistry 49 25 (2010): 5097-5108.
    10.1021/bi100410q
  245. Dourado, Dfar; Fernandes, P. A.; Ramos, M. J.. "Glutathione Transferase Classes Alpha, Pi, and Mu: GSH Activation Mechanism". Journal of Physical Chemistry B 114 40 (2010): 12972-12980.
    10.1021/jp1053875
  246. Barbosa, A. J. M.; De Rienzo, F.; Ramos, M. J.; Menziani, M. C.. "Computational analysis of ligand recognition sites of homo- and heteropentameric 5-HT3 receptors". European Journal of Medicinal Chemistry 45 11 (2010): 4746-4760. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000283911300007&KeyUID=WOS:000283911300007.
    10.1016/j.ejmech.2010.07.039
  247. Ramos, M. J.. "Computational enzymatic catalysis". Febs Journal 277 (2010): 25-25. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000278565100097&KeyUID=WOS:000278565100097.
    10.1021/ar7001045
  248. Ribeiro, A. J. M.; Ramos, M. J.; Fernandes, P. A.. "Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds". Journal of Chemical Theory and Computation 6 8 (2010): 2281-2292. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000280661600003&KeyUID=WOS:000280661600003.
    10.1021/ct900649e
  249. Cruz, L.; Bras, N. F.; Teixeira, N.; Mateus, N.; Ramos, M. J.; Dangles, O.; De Freitas, V.. "Vinylcatechin Dimers Are Much Better Copigments for Anthocyanins than Catechin Dimer Procyanidin B3". Journal of Agricultural and Food Chemistry 58 5 (2010): 3159-3166. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000275087600080&KeyUID=WOS:000275087600080.
    10.1021/jf9037419
  250. Sousa, S. F.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Virtual Screening in Drug Design and Development". Combinatorial Chemistry & High Throughput Screening 13 5 (2010): 442-453. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000277889700008&KeyUID=WOS:000277889700008.
    10.2174/138620710791293001
  251. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "QM/MM Studies on the beta-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions". Journal of Chemical Theory and Computation 6 2 (2010): 421-433. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000274838800008&KeyUID=WOS:000274838800008.
    10.1021/ct900530f
  252. Bras, N. F.; Goncalves, R.; Mateus, N.; Fernandes, P. A.; Ramos, M. J.; Do Freitas, V.. "Inhibition of Pancreatic Elastase by Polyphenolic Compounds". Journal of Agricultural and Food Chemistry 58 19 (2010): 10668-10676. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000282545000051&KeyUID=WOS:000282545000051.
    10.1021/jf1017934
  253. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Gas-phase geometry optimization of biological molecules as a reasonable alternative to a continuum environment description: Fact, myth, or fiction?". Journal of Physical Chemistry A 113 52 (2009): 14231-14236. http://www.scopus.com/inward/record.url?eid=2-s2.0-73949129042&partnerID=MN8TOARS.
    10.1021/jp902213t
  254. Sousa, S.F.; Fernandes, P.A.; Rãmos, M.J.. "The search for the mechanism of the reaction catalyzed by farnesyltransferase". Chemistry - A European Journal 15 17 (2009): 4243-4247. http://www.scopus.com/inward/record.url?eid=2-s2.0-65349137563&partnerID=MN8TOARS.
    10.1002/chem.200802745
  255. Cruz, L.; Brás, N.F.; Teixeira, N.; Fernandes, A.N.A.; Mateus, N.; Ramos, M.J.; Rodríguez-Borges, J.; De Freitas, V.. "Synthesis and structural characterization of two diasteroisomers of vinylcatechin dimers". Journal of Agricultural and Food Chemistry 57 21 (2009): 10341-10348. http://www.scopus.com/inward/record.url?eid=2-s2.0-70449120689&partnerID=MN8TOARS.
    10.1021/jf901608n
  256. Silva, P.J.; Ramos, M.J.. "Computational studies on the reactivity of substituted 1,2-dihydro-1,2- azaborines". Journal of Organic Chemistry 74 16 (2009): 6120-6129. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349098090&partnerID=MN8TOARS.
    10.1021/jo900980d
  257. Pande, V.; Sousa, S.F.; Ramos, M.J.. "Direct covalent modification as a strategy to inhibit Nuclear Factor-Kappa B". Current Medicinal Chemistry 16 32 (2009): 4261-4273. http://www.scopus.com/inward/record.url?eid=2-s2.0-70450198853&partnerID=MN8TOARS.
    10.2174/092986709789578222
  258. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme". Bioorganic & Medicinal Chemistry 17 9 (2009): 3369-3378.
    10.1016/j.bmc.2009.03.055
  259. Sousa, S. F.; Carvalho, E. S.; Ferreira, D. M.; Tavares, I. S.; Fernandes, P. A.; Ramos, M. J.; Gomes, Janf; et al. "Comparative Analysis of the Performance of Commonly Available Density Functionals in the Determination of Geometrical Parameters for Zinc Complexes". Journal of Computational Chemistry 30 16 (2009): 2752-2763. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000322703400003&KeyUID=WOS:000322703400003.
    10.1002/jcc.21304
  260. Sousa, S.F.; Cerqueira, N.M.F.S.A.; Perez, M.A.S.; Moreira, I.S.; Ribeiro, A.J.M.; Neves, A.R.A.P.; Ramos, M.J.; Fernandes, P.A.. "Recent advances on computational proteomics". World Academy of Science, Engineering and Technology 56 (2009): 376-386. http://www.scopus.com/inward/record.url?eid=2-s2.0-78651571830&partnerID=MN8TOARS.
  261. Cerqueira, N.M.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Virtual screening of compound libraries.". Methods in molecular biology (Clifton, N.J.) 572 (2009): 57-70. http://www.scopus.com/inward/record.url?eid=2-s2.0-79952110876&partnerID=MN8TOARS.
    10.1007/978-1-60761-244-5_4
  262. Marques, A.T.; Fernandes, P.A.; Ramos, M.J.. "ABAD: A potential therapeutic target for Aß-induced mitochondrial dysfunction in Alzheimer's disease". Mini-Reviews in Medicinal Chemistry 9 8 (2009): 1002-1008. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349090165&partnerID=MN8TOARS.
  263. Sousa, S. F.; Lopes, A. B.; Fernandes, P. A.; Ramos, M. J.. "The Zinc proteome: a tale of stability and functionality". Dalton Transactions 38 (2009): 7946-7956.
    10.1039/b904404c
  264. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Docking and molecular dynamics studies on the stereoselectivity in the enzymatic synthesis of carbohydrates". Theoretical Chemistry Accounts 122 5-6 (2009): 283-296.
    10.1007/s00214-009-0507-2
  265. Cerqueira, Nmfsa; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "MADAMM: A multistaged docking with an automated molecular modeling protocol". Proteins-Structure Function and Bioinformatics 74 1 (2009): 192-206. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000261757900017&KeyUID=WOS:000261757900017.
    10.1002/prot.22146
  266. Moura-Tamames, S.; Ramos, M. J.; Fernades, P. A.; Moura-Tamames, S. A.; Fernandes, P. A.. "Modelling beta-1,3-Exoglucanase- saccharide interactions: structure of the enzyme-substrate complex and enzyme binding to the cell wall". Febs Journal 276 8 (2009): 156-157. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000267069900446&KeyUID=WOS:000267069900446.
    10.1016/j.jmgm.2009.01.007
  267. Dourado, Dfar; Fernandes, P. A.; Ramos, M. J.. "Glutathione transferase A1-1: catalytic role of water". Theoretical Chemistry Accounts 124 1-2 (2009): 71-83. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000269219100007&KeyUID=WOS:000269219100007.
    10.1007/s00214-009-0582-4
  268. Tamames, B.; Fernandes, P. A.; Ramos, M. J.. "HIV-1 Protease: a computational mutagenesis analysis of the monomers interface". Febs Journal 276 (2009): 167-167. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000267069900481&KeyUID=WOS:000267069900481.
  269. Moura-Tamames, S. A.; Ramos, M. J.; Fernades, P. A.. "Exploring beta-1,3-Exoglucanase-polysaccharide interactions: molecular dynamics of the enzyme-substrate complex with or without a polysaccharide ligand bound in the flexible enzyme loops". Febs Journal 276 (2009): 156-156. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000267069900445&KeyUID=WOS:000267069900445.
  270. Carvalho, A. T. P.; Fernandes, P. A.; Swart, M.; van Stralen, J. N. P.; Bickelhaupt, F. M.; Ramos, M. J.. "Role of the Variable Active Site Residues in the Function of Thioredoxin Family Oxidoreductases". Journal of Computational Chemistry 30 5 (2009): 710-724. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000264225900003&KeyUID=WOS:000264225900003.
    10.1002/jcc.21086
  271. Silva, P.J.; Ramos, M.J.. "A comparative density-functional study of the reaction mechanism of the O2-dependent coproporphyrinogen III oxidase". Bioorganic and Medicinal Chemistry 16 6 (2008): 2726-2733. http://www.scopus.com/inward/record.url?eid=2-s2.0-40949117609&partnerID=MN8TOARS.
    10.1016/j.bmc.2008.01.008
  272. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Enzyme flexibility and the catalytic mechanism of farnesyltransferase: Targeting the relation". Journal of Physical Chemistry B 112 29 (2008): 8681-8691. http://www.scopus.com/inward/record.url?eid=2-s2.0-49149110925&partnerID=MN8TOARS.
    10.1021/jp711214j
  273. da Fonseca, R. R.; Johnson, W. E.; O'Brien, S. J.; Ramos, M. J.; Antunes, A.. "The adaptive evolution of the mammalian mitochondrial genome". Bmc Genomics 9 (2008):
    10.1186/1471-2164-9-119
  274. Martins, S.; Ramos, M. J.; Fernandes, P. A.. "The current status of the NNRTI family of antiretrovirals used in the HAART regime against HIV infection". Current Medicinal Chemistry 15 11 (2008): 1083-1095.
    10.2174/092986708784221467
  275. Dourado, Dfar; Fernandes, P. A.; Mannervik, B.; Ramos, M. J.. "Glutathione Transferase: New Model for Glutathione Activation". Chemistry-a European Journal 14 31 (2008): 9591-9598.
    10.1002/chem.200800946
  276. Pande, V.; Ramos, M. J.; Gago, F.. "The protein kinase inhibitor balanol: Structure-activity relationships and structure-based computational studies". Anti-Cancer Agents in Medicinal Chemistry 8 6 (2008): 638-645. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000258737800006&KeyUID=WOS:000258737800006.
  277. Russo, N.; Ramos, M. J.; Ugalde, J. M.; Eriksson, L. A.. "Special issue: Proceedings of the 3rd Theoretical Biophysics Symposium - Centraro, Italy, June 16-20, 2007 - Introduction". International Journal of Quantum Chemistry 108 11 (2008): 1-1. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000257642300001&KeyUID=WOS:000257642300001.
    10.1002/qua.21776
  278. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Farnesyltransferase inhibitors: A detailed chemical view on an elusive biological problem". Current Medicinal Chemistry 15 15 (2008): 1478-1492.
    10.2174/092986708784638825
  279. Preto, M. A. C.; Melo, A.; Rodrigues, L. M.; Maia, H. L. S.; Ramos, M. J.. "Structural Insight on the Activity of Type 1 Angiotensin II Peptide Antagonists Using MD Simulations". Journal of Physical Chemistry B 112 43 (2008): 13620-13628. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000260357700020&KeyUID=WOS:000260357700020.
    10.1021/jp802349w
  280. Dourado, Dfar; Fernandes, P. A.; Ramos, M. J.. "Mammalian cytosolic glutathione transferases". Current Protein & Peptide Science 9 4 (2008): 325-337. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000259487200002&KeyUID=WOS:000259487200002.
    10.2174/138920308785132677
  281. Carvalho, A. T. P.; Swart, M.; van Stralen, J. N. P.; Fernandes, P. A.; Ramos, M. J.; Bickelhaupt, F. M.. "Mechanism of thioredoxin-catalyzed disulfide reduction. Activation of the buried thiol and role of the variable active-site residues". Journal of Physical Chemistry B 112 8 (2008): 2511-2523. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000253355500025&KeyUID=WOS:000253355500025.
    10.1021/jp7104665
  282. Bras, N. F.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Carbohydrate-binding modules from family 11: Understanding the binding mode of polysaccharides". International Journal of Quantum Chemistry 108 11 (2008): 2030-2040. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000257642300016&KeyUID=WOS:000257642300016.
    10.1002/qua.21755
  283. Branco, R. J. F.; Seifert, A.; Budde, M.; Urlacher, V. B.; Ramos, M. J.; Pleiss, J.. "Anchoring effects in a wide binding pocket: The molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium". Proteins-Structure Function and Bioinformatics 73 3 (2008): 597-607. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000260515500006&KeyUID=WOS:000260515500006.
    10.1002/prot.22083
  284. Silva, P. J.; Ramos, M. J.. "Comparative density functional study of models for the reaction mechanism of uroporphyrinogen III synthase". Journal of Physical Chemistry B 112 10 (2008): 3144-3148.
    10.1021/jp076235f
  285. Marques, A. T.; Antunes, A.; Fernandes, P. A.; Ramos, M. J.. "Computational optimization of AG18051 inhibitor for amyloid-beta binding alcohol dehydrogenase enzyme". International Journal of Quantum Chemistry 108 11 (2008): 1982-1991.
    10.1002/qua.21716
  286. Ramos, M. J.; Fernandes, P. A.. "Computational enzymatic catalysis". Accounts of Chemical Research 41 6 (2008): 689-698.
    10.1021/ar7001045
  287. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Protein-protein recognition: a computational mutagenesis study of the MDM2-P53 complex". Theoretical Chemistry Accounts 120 4-6 (2008): 533-542.
    10.1007/s00214-008-0432-9
  288. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Molecular dynamics analysis of farnesyltransferase: A closer look into the amino acid behavior". International Journal of Quantum Chemistry 108 11 (2008): 1939-1950.
    10.1002/qua.21713
  289. Marques, A. T.; Fernandes, P. A.; Ramos, M. J.. "Molecular dynamics simulations of the amyloid-beta binding alcohol dehydrogenase (ABAD) enzyme". Bioorganic & Medicinal Chemistry 16 21 (2008): 9511-9518.
    10.1016/j.bmc.2008.09.043
  290. Bras, N. F.; Moura-Tamames, S. A.; Fernandes, P. A.; Ramos, M. J.. "Mechanistic Studies on the Formation of Glycosidase-Substrate and Glycosidase-Inhibitor Covalent Intermediates". Journal of Computational Chemistry 29 15 (2008): 2565-2574.
    10.1002/jcc.21013
  291. Viegas, A.; Bras, N. F.; Cerqueira, Nmfsa; Fernandes, P. A.; Prates, J. A. M.; Fontes, Cmga; Bruix, M.; et al. "Molecular determinants of ligand specificity in family 11 carbohydrate binding modules - an NMR, X-ray crystallography and computational chemistry approach". Febs Journal 275 10 (2008): 2524-2535.
    10.1111/j.1742-4658.2008.06401.x
  292. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Comparative assessment of theoretical methods for the determination of geometrical properties in biological zinc complexes". Journal of Physical Chemistry B 111 30 (2007): 9146-9152.
    10.1021/jp072538y
  293. Luo, S.-J.; Cai, Q.-X.; David, V.A.; Zhang, L.; Martelli, P.; Lim, N.T.-L.; Ferrand, N.; et al. "Erratum: Isolation and characterization of microsatellite markers in pangolins (Mammalia, Pholidota, Manis spp.) (Molecular Ecology Notes (2006) 7 (269-272))". Molecular Ecology Notes 7 3 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-34248209102&partnerID=MN8TOARS.
    10.1111/j.1471-8286.2007.01778.x
  294. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Vascular endothelial growth factor (VEGF) inhibition - A critical review". Anti-Cancer Agents in Medicinal Chemistry 7 2 (2007): 223-245. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000244009200005&KeyUID=WOS:000244009200005.
    10.2174/187152007780058687
  295. Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Ribonucleotide reductase: A critical enzyme for cancer chemotherapy and antiviral agents". Recent Patents on Anti-Cancer Drug Discovery 2 1 (2007): 11-29. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000246564300002&KeyUID=WOS:000246564300002.
    10.2174/157489207779561408
  296. Antunes, A.; Ramos, M. J.. "Gathering Computational Genomics and Proteomics to Unravel Adaptive Evolution". Evolutionary Bioinformatics 3 (2007): 207-209. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000206500600016&KeyUID=WOS:000206500600016.
  297. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Computational alanine scanning mutagenesis - An improved methodological approach". Journal of Computational Chemistry 28 3 (2007): 644-654.
    10.1002/jcc.20566
  298. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "General performance of density functionals". Journal of Physical Chemistry A 111 42 (2007): 10439-10452.
    10.1021/jp0734474
  299. Perez, M. A. S.; Fernandes, P. A.; Ramos, M. J.. "Drug design: New inhibitors for HIV-1 protease based on Nelfinavir as lead". Journal of Molecular Graphics & Modelling 26 3 (2007): 634-642.
    10.1016/j.jmgm.2007.03.009
  300. Santos, H. R. R.; Ujaque, G.; Ramos, M. J.; Gomes, Janf. "Effect of the tert-butiloxycarbonyl protecting group on the adsorption of protected amino-cyclopentene on the Si(100) surface". Physical Review B 75 12 (2007):
    10.1103/PhysRevB.75.125413
  301. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL-10". International Journal of Quantum Chemistry 107 2 (2007): 299-310.
    10.1002/qua.21193
  302. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism". Theoretical Chemistry Accounts 117 1 (2007): 171-181.
    10.1007/s00214-006-0170-9
  303. Tamames, B.; Sousa, S. F.; Tamames, J.; Fernandes, P. A.; Ramos, M. J.. "Analysis of zinc-ligand bond lengths in metalloproteins: Trends and patterns". Proteins-Structure Function and Bioinformatics 69 3 (2007): 466-475.
    10.1002/prot.21536
  304. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Backbone importance for protein-protein binding". Journal of Chemical Theory and Computation 3 3 (2007): 885-893.
    10.1021/ct6003824
  305. Antunes, A.; Pontius, J.; Ramos, M. J.; O'Brien, S. J.; Johnson, W. E.. "Mitochondrial introgressions into the nuclear genome of the domestic cat". Journal of Heredity 98 5 (2007): 414-420.
    10.1093/jhered/esm062
  306. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "Parameterization of AZT - A widely used nucleoside inhibitor of HIV-1 reverse transcriptase". International Journal of Quantum Chemistry 107 2 (2007): 292-298.
    10.1002/qua.21192
  307. Luo, S. J.; Cai, Q. X.; David, V. A.; Zhang, L.; Martelli, P.; Lim, N. T. L.; Ferrand, N.; et al. "Isolation and characterization of microsatellite markers in pangolins (Mammalia, Pholidota, Manis spp.)". Molecular Ecology Notes 7 2 (2007): 269-272.
    10.1111/j.1471-8286.2006.01577.x
  308. Santos, H. R. R.; Ramos, M. J.; Gomes, Janf. "Microscopic detail provided for the adsorption of protected amino-cyclopentene on Si(100)". Chemical Physics Letters 448 1-3 (2007): 111-114.
    10.1016/j.cplett.2007.09.064
  309. Osorio, D. S.; Antunes, A.; Ramos, M. J.. "Structural and functional implications of positive selection at the primate angiogenin gene". Bmc Evolutionary Biology 7 (2007):
    10.1186/1471-2148-7-167
  310. Silva, P. J.; Ramos, M. J.. "Reaction mechanism of the vitamin K-dependent glutamate carboxylase: A computational study". Journal of Physical Chemistry B 111 44 (2007): 12883-12887.
    10.1021/jp0738208
  311. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Hot spot occlusion from bulk water: A comprehensive study of the complex between the lysozyme HEL and the antibody FVD1.3". Journal of Physical Chemistry B 111 10 (2007): 2697-2706.
    10.1021/jp067096p
  312. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Hot spots-A review of the protein-protein interface determinant amino-acid residues". Proteins-Structure Function and Bioinformatics 68 4 (2007): 803-812.
    10.1002/prot.21396
  313. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "The excision mechanism in reverse transcriptase: Pyrophosphate leaving and fingers opening are uncoupled events with the analogues AZT and d4T". Journal of Physical Chemistry B 111 41 (2007): 12032-12039.
    10.1021/jp0746594
  314. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Theoretical studies on farnesyltransferase: Evidence for thioether product coordination to the active-site zinc sphere". Journal of Computational Chemistry 28 7 (2007): 1160-1168.
    10.1002/jcc.20577
  315. da Fonseca, R. R.; Antunes, A.; Melo, A.; Ramos, M. J.. "Structural divergence and adaptive evolution in mammalian cytochromes P4502C". Gene 387 1-2 (2007): 58-66.
    10.1016/j.gene.2006.08.017
  316. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "The carboxylate shift in zinc enzymes: A computational study". Journal of the American Chemical Society 129 5 (2007): 1378-1385.
    10.1021/ja067103n
  317. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Unravelling Hot Spots: a comprehensive computational mutagenesis study". Theoretical Chemistry Accounts 117 1 (2007): 99-113.
    10.1007/s00214-006-0151-z
  318. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Theoretical studies on farnesyltransferase: The distances paradox explained". Proteins-Structure Function and Bioinformatics 66 1 (2007): 205-218.
    10.1002/prot.21219
  319. Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. L.. "Understanding ribonucleotide reductase inactivation by gemcitabine". Chemistry-a European Journal 13 30 (2007): 8507-8515.
    10.1002/chem.200700260
  320. Carvalho, A.T.P.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics model of unliganded HIV-1 reverse transcriptase". Medicinal Chemistry 2 5 (2006): 491-498. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748677715&partnerID=MN8TOARS.
    10.2174/157340606778250270
  321. da Fonseca, R.; Melo, A.; Iori, F.; Menziani, C.; Ramos, M.J.. "Molecular interactions between human cytochrome P450 1A2 and flavone derivatives". Medicinal Chemistry 2 4 (2006): 401-406. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746110349&partnerID=MN8TOARS.
    10.2174/157340606777723988
  322. Marques, A. T.; Antunes, A.; Fernandes, P. A.; Ramos, M. J.. "Comparative evolutionary genomics of the HADH2 gene encoding A beta-binding alcohol dehydrogenase/17 beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10)". Bmc Genomics 7 (2006):
    10.1186/1471-2164-7-202
  323. Pereira, S.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Computational studies on class I ribonucleotide reductase: Understanding the mechanisms of action and inhibition of a cornerstone enzyme for the treatment of cancer". European Biophysics Journal with Biophysics Letters 35 2 (2006): 125-135.
    10.1007/s00249-005-0026-6
  324. Ramos, M. J.; Fernandes, P. A.. "Atomic-Level Rational Drug Design". Current Computer-Aided Drug Design 2 1 (2006): 57-81.
    10.2174/157340906776056464
  325. Sharma, R. K.; Chopra, S.; Sharma, S. D.; Pande, V.; Ramos, M. J.; Meguro, K.; Inoue, J. I.; Otsuka, M.. "Biological evaluation, chelation, and molecular modeling studies of novel metal-chelating inhibitors of NF-kappa B-DNA binding: Structure activity relationships". Journal of Medicinal Chemistry 49 12 (2006): 3595-3601.
    10.1021/jm050617x
  326. Cerqueira, Nmfsa; Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "Dehydration of ribonucleotides catalyzed by ribonucleotide reductase: The role of the enzyme". Biophysical Journal 90 6 (2006): 2109-2119.
    10.1529/biophysj.104.054627
  327. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Detailed microscopic study of the full ZipA : FtsZ interface". Proteins-Structure Function and Bioinformatics 63 4 (2006): 811-821.
    10.1002/prot.20944
  328. Henriques, E. S.; Nascimento, M. A. C.; Ramos, M. J.. "Computational study of some benzamidine-based inhibitors of thrombin-like snake venom proteinases". International Journal of Quantum Chemistry 106 9 (2006): 2107-2121.
    10.1002/qua.20999
  329. Branco, R. J. F.; Fernandes, P. A.; Ramos, M. J.. "Cu, Zn Superoxide dismutase: distorted active site binds substrate without significant energetic cost". Theoretical Chemistry Accounts 115 1 (2006): 27-31.
    10.1007/s00214-005-0672-x
  330. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "Theoretical study of the unusual protonation properties of the active site cysteines in thioredoxin". Journal of Physical Chemistry B 110 11 (2006): 5758-5761.
    10.1021/jp053275f
  331. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Unraveling the importance of protein-protein interaction: Application of a computational alanine-scanning mutagenesis to the study of the IgG1 streptococcal protein G (C2 fragment) complex". Journal of Physical Chemistry B 110 22 (2006): 10962-10969.
    10.1021/jp054760d
  332. Santos, H. R. R.; Ujaque, G.; Ramos, M. J.; Gomes, Janf. "QM/QM study of the coverage effects on the adsorption of amino-cyclopentene at the Si(100) surface". Journal of Computational Chemistry 27 15 (2006): 1892-1897.
    10.1002/jcc.20513
  333. Carvalho, A. P.; Fernandes, P. A.; Ramos, M. J.. "Similarities and differences in the thioredoxin superfamily". Progress in Biophysics & Molecular Biology 91 3 (2006): 229-248.
    10.1016/j.pbiomolbio.2005.06.012
  334. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "Insights on resistance to reverse transcriptase: The different patterns of interaction of the nucleoside reverse transcriptase inhibitors in the deoxyribonucleotide triphosphate binding site relative to the normal substrate". Journal of Medicinal Chemistry 49 26 (2006): 7675-7682.
    10.1021/jm060698c
  335. Fernandes, P. A.; Araujo, Mlac; Barbosa, A. J. M.; Alves, C. N.; Ferreira, Z. Q.; Gonzalez, C. R. N.; Lima, Cfrac; et al. "Lead optimisation: Improving the affinity of the antiretrovirals Nelfinavir and Amprenavir for HIV-1 protease". Letters in Drug Design & Discovery 3 6 (2006): 383-389.
    10.2174/157018006777805576
  336. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "Determination of the Delta pKa between the active site cysteines of thioredoxin and DsbA". Journal of Computational Chemistry 27 8 (2006): 966-975.
    10.1002/jcc.20404
  337. Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Enzyme ribonucleotide reductase: Unraveling an enigmatic paradigm of enzyme inhibition by furanone derivatives". Journal of Physical Chemistry B 110 42 (2006): 21272-21281.
    10.1021/jp0608269
  338. Carvalho, A. P.; Fernandes, P. A.; Ramos, M. J.. "Molecular insights into the mechanisms of HIV-1 reverse transcriptase resistance to nucleoside analogs". Mini-Reviews in Medicinal Chemistry 6 5 (2006): 549-555.
    10.2174/138955706776876276
  339. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Protein-ligand docking: Current status and future challenges". Proteins-Structure Function and Bioinformatics 65 1 (2006): 15-26.
    10.1002/prot.21082
  340. Lucas, M. F.; Ramos, M. J.. "Mechanism of a soluble fumarate reductase from Shewanella frigidimarina: A theoretical study". Journal of Physical Chemistry B 110 21 (2006): 10550-10556.
    10.1021/jp057456t
  341. Branco, R. J. F.; Fernandes, P. A.; Ramos, M. J.. "Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase". Journal of Physical Chemistry B 110 33 (2006): 16754-16762.
    10.1021/jp056855l
  342. Ramos, M. J.; Fernandes, P. A.. "Computer modeling and research in the classroom". Journal of Chemical Education 82 7 (2005): 1021-1025. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000229773400017&KeyUID=WOS:000229773400017.
  343. da Fonseca, R.; Marini, M.; Melo, A.; Menziani, M. C.; Ramos, M. J.. "Computational Insight into Anti-mutagenic Properties of CYP1A Flavonoid Ligands". Medicinal Chemistry 1 4 (2005): 355-360. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000208266000004&KeyUID=WOS:000208266000004.
    10.2174/1573406054368729
  344. Pande, V.; Ramos, M.J.. "NF-¿B in human disease: Current inhibitors and prospects for De Novo structure based design of inhibitors". Current Medicinal Chemistry 12 3 (2005): 357-374. http://www.scopus.com/inward/record.url?eid=2-s2.0-14544269951&partnerID=MN8TOARS.
  345. Fernandes, P. A.; Maia, A. R. R.; Almeida, A. A. S.; Silva, B. F. B.; Ribeiro, C. M. S.; Ribeiro, C. F. B.; Ribeiro, D. S. M.; et al. "New designs for inhibitors of the NF-kappa B: DNA binding". Theoretical Chemistry Accounts 113 4 (2005): 197-204.
    10.1007/s00214-005-0628-1
  346. Preto, M. A. C.; Melo, A.; Maia, H. L. S.; Mavromoustakos, T.; Ramos, M. J.. "Molecular dynamics simulations of angiotensin II in aqueous and dimethyl sulfoxide environments". Journal of Physical Chemistry B 109 37 (2005): 17743-17751.
    10.1021/jp0521048
  347. Pande, V.; Ramos, M. J.. "Molecular recognition of 15-deoxy-Delta(12,14)-prostaglandin J(2) by nuclear factor-kappa B and other cellular proteins". Bioorganic & Medicinal Chemistry Letters 15 18 (2005): 4057-4063.
    10.1016/j.bmcl.2005.06.025
  348. Ramos, M. J.; Magalhaes, A. L.; Melo, A. S.; Fernandes, P. A.. "Special issue: A collection of papers presented at the 30th international congress of theoretical chemists of Latin Expression, Porto, Portugal, 8-12 September 2004 - Foreword". Journal of Molecular Structure-Theochem 729 1-2 (2005): VII-VII.
    10.1016/j.theochem.2005.04.028
  349. Pande, V.; Ramos, M. J.. "Structural basis for the GSK-3 beta binding affinity and selectivity against CDK-2 of 1-(4-aminofurazan-3yl)-5-dialkylaminomethyl-1-H- 1,2,3 triazole-4-carboxylic acid derivatives". Bioorganic & Medicinal Chemistry Letters 15 23 (2005): 5129-5135.
    10.1016/j.bmcl.2005.08.077
  350. Cerqueira, Nmfsa; Pereira, S.; Fernandes, P. A.; Ramos, M. J.. "Overview of ribonucleotide reductase inhibitors: An appealing target in anti-tumour therapy". Current Medicinal Chemistry 12 11 (2005): 1283-1294.
    10.2174/0929867054020981
  351. Branco, R. J. F.; Fernandes, P. A.; Ramos, M. J.. "Density-functional calculations of the Cu, Zn superoxide dismutase redox potential: The influence of active site distortion". Journal of Molecular Structure-Theochem 729 1-2 (2005): 141-146.
    10.1016/j.theochem.2004.12.046
  352. Silva, P. J.; Ramos, M. J.. "Density-functional study of mechanisms for the cofactor-free decarboxylation performed by uroporphyrinogen III decarboxylase". Journal of Physical Chemistry B 109 38 (2005): 18195-18200.
    10.1021/jp051792s
  353. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Farnesyltransferase: Theoretical studies on peptide substrate entrance thiol or thiolate coordination?". Journal of Molecular Structure-Theochem 729 1-2 (2005): 125-129.
    10.1016/j.theochem.2005.03.022
  354. Sharma, R. K.; Pande, V.; Ramos, M. J.; Rajor, H. K.; Chopra, S.; Meguro, K.; Inoue, J.; Otsuka, M.. "Inhibitory activity of polyhydroxycarboxylate chelators against recombinant NF-kappa B p50 protein-DNA binding". Bioorganic Chemistry 33 2 (2005): 67-81.
    10.1016/j.bioorg.2004.12.001
  355. Antunes, A.; Ramos, M. J.. "Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes". Genomics 86 6 (2005): 708-717.
    10.1016/j.ygeno.2005.08.002
  356. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Farnesyltransferase - New insights into the zinc-coordination sphere paradigm: Evidence for a carboxylate-shift mechanism". Biophysical Journal 88 1 (2005): 483-494.
    10.1529/biophysj.104.048207
  357. Pereira, S.; Fernandes, P. A.; Ramos, M. J.. "Theoretical study on the inhibition of ribonucleotide reductase by 2 '-mercapto-2 '-deoxyribonucleoside-5 '-diphosphates". Journal of the American Chemical Society 127 14 (2005): 5174-5179.
    10.1021/ja046662w
  358. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Unraveling the mechanism of the farnesyltransferase enzyme". Journal of Biological Inorganic Chemistry 10 1 (2005): 3-10.
    10.1007/s00775-004-0612-6
  359. Iori, F.; da Fonseca, R.; Ramos, M. J.; Menziani, M. C.. "Theoretical quantitative structure-activity relationships of flavone ligands interacting with cytochrome P450 1A1 and 1A2 isozymes". Bioorganic & Medicinal Chemistry 13 14 (2005): 4366-4374.
    10.1016/j.bmc.2005.04.066
  360. Lucas, M. D.; Ramos, M. J.. "Theoretical study of the suicide inhibition mechanism of the enzyme pyruvate formate lyase by methacrylate". Journal of the American Chemical Society 127 18 (2005): 6902-6909.
    10.1021/ja047699j
  361. Santos, H. R. R.; Ramos, M. J.; Gomes, Janf. "Adsorption of protected and unprotected amino-cyclopentene at the Si(100) surface modeled with a hybrid quantum mechanical cluster technique". Physical Review B 72 7 (2005):
    10.1103/physrevb.72.075445
  362. Santos, H. R. R.; Ramos, M. J.; Gomes, Janf. "A new strategy to model the Si(100) surface". Comptes Rendus Chimie 8 9-10 (2005): 1461-1468.
    10.1016/j.crci.2004.10.033
  363. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Accuracy of the numerical solution of the Poisson-Boltzmann equation". Journal of Molecular Structure-Theochem 729 1-2 (2005): 11-18.
    10.1016/j.theochem.2004.12.049
  364. Ramos, M. J.; Fernandes, P. A.; Melo, A.. "Modeling chemical and biological systems: A successful course for undergraduate students". Journal of Chemical Education 81 1 (2004): 72-75. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000187308400030&KeyUID=WOS:000187308400030.
    10.1021/ed081p72
  365. Henriques, E. S.; Fonseca, N.; Ramos, M. J.. "On the modeling of snake venom serine proteinase interactions with benzamidine-based thrombin inhibitors". Protein Science 13 9 (2004): 2355-2369.
    10.1110/ps.04746804
  366. Cerqueira, Nmfsa; Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzyme". Journal of Computational Chemistry 25 16 (2004): 2031-2037.
    10.1002/jcc.20127
  367. Cerqueira, Nmfsa; Femandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "New insights into a critical biological control step of the mechanism of Ribonucleotide reductase". Journal of Molecular Structure-Theochem 709 1-3 (2004): 53-65.
    10.1016/j.theochem.2003.10.073
  368. Fernandes, P. A.; Ramos, M. J.. "Theoretical insights into the mechanism for thiol/disulfide exchange". Chemistry-a European Journal 10 1 (2004): 257-266.
    10.1002/chem.200305343
  369. Pereira, S.; Fernandes, P. A.; Ramos, M. J.. "Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2 '-azido-2 '-deoxyribonucleoside 5-diphosphates". Journal of Computational Chemistry 25 2 (2004): 227-237.
    10.1002/jcc.10375
  370. Sharma, R. K.; Otsuka, M.; Pande, V.; Inoue, J.; Ramos, M. J.. "Evans Blue is an inhibitor of nuclear factor-kappa B (NF-kappa B)-DNA binding". Bioorganic & Medicinal Chemistry Letters 14 24 (2004): 6123-6127.
    10.1016/j.bmcl.2004.07.096
  371. Pereira, S.; Fernandes, P. A.; Ramos, M. J.. "Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine". Journal of Computational Chemistry 25 10 (2004): 1286-1294.
    10.1002/jcc.20054
  372. Portela, C.; Afonso, C. M. M.; Pinta, M. M. M.; Ramos, M. J.. "Definition of an electronic profile of compounds with inhibitory activity against hematin aggregation in malaria parasite". Bioorganic & Medicinal Chemistry 12 12 (2004): 3313-3321.
    10.1016/j.bmc.2004.03.060
  373. Fernandes, P. A.; Cruz, A. I. S.; Maia, A. R. R.; Almeida, A. A. S.; da Silva, A. M. N.; Silva, B. F. B.; Ribeiro, C. M. S.; et al. "Design of 2-cyclopentenone derivatives with enhanced NF-kappa B: DNA binding inhibitory properties". Journal of Molecular Structure-Theochem 685 1-3 (2004): 73-82.
    10.1016/j.theochem.2004.06.027
  374. Fernandes, P. A.; Ramos, M. J.. "Theoretical studies on the mode of inhibition of ribonucleotide reductase by 2 '-substituted substrate analogues". Chemistry-a European Journal 9 23 (2003): 5916-5925.
    10.1002/chem.200304948
  375. Henriques, E. S.; Bastos, M.; Geraldes, Cfgc; Ramos, M. J.. "Studies of inclusion complexes between cyclodextrins and polyazamacrocyclic chelates of lanthanide(III) ions". Journal of Chemical Thermodynamics 35 10 (2003): 1717-1735.
    10.1016/s0021-9614(03)00160-5
  376. Fernandes, P. A.; Ramos, M. J.. "Theoretical studies on the mechanism of inhibition of ribonucleotide reductase by (E)-2 '-fluoromethylene-2 '-deoxycitidine-5 '-diphosphate". Journal of the American Chemical Society 125 20 (2003): 6311-6322.
    10.1021/ja0208613
  377. Da Fonseca, R.; Menziani, M. C.; Melo, A.; Ramos, M. J.. "Modelling the metabolic action of human and rat CYP1A2 and its relationship with the carcinogenicity of heterocyclic amines". Molecular Physics 101 17 (2003): 2731-2741.
    10.1080/00268970310001603112
  378. Fernandes, P. A.; Carvalho, A. T. P.; Marques, A. T.; Pereira, A. L. F.; Madeira, A. P. S.; Ribeiro, A. S. P.; Carvalho, A. F. R.; et al. "New designs for MRI contrast agents". Journal of Computer-Aided Molecular Design 17 7 (2003): 463-473.
    10.1023/A:1027347527385
  379. Portela, C.; Afonso, C. M. M.; Pinto, M. M. M.; Ramos, M. J.. "Computational studies of new potential antimalarial compounds - Stereoelectronic complementarity with the receptor". Journal of Computer-Aided Molecular Design 17 9 (2003): 583-595.
    10.1023/b:jcam.0000005754.24588.a0
  380. Henriques, E. S.; Geraldes, Cfgc; Ramos, M. J.. "Modelling studies in aqueous solution of lanthanide (III) chelates designed for nuclear magnetic resonance biomedical applications". Molecular Physics 101 15 (2003): 2319-2333.
    10.1080/0026897031000108023
  381. Lucas, M. D.; Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "Pyruvate formate lyase: A new perspective". Journal of Physical Chemistry B 107 24 (2003): 5751-5757.
    10.1021/jp0223096
  382. Portela, C.; Afonso, C. M. M.; Pinto, M. M. M.; Ramos, M. J.. "Receptor-drug association studies in the inhibition of the hematin aggregation process of malaria". Febs Letters 547 1-3 (2003): 217-222.
    10.1016/s0014-5793(03)00692-6
  383. Pande, V.; Ramos, M. J.. "Nuclear Factor Kappa B: A potential target for anti-HIV chemotherapy". Current Medicinal Chemistry 10 16 (2003): 1603-1615.
    10.2174/0929867033457250
  384. Preto, M. A. C.; Melo, A.; Costa, S. P. G.; Maia, H. L. S.; Ramos, M. J.. "Parametrization of synthetic amino acids". Journal of Physical Chemistry B 107 51 (2003): 14556-14562.
    10.1021/jp030544y
  385. Pande, V.; Sharma, R. K.; Inoue, J. I.; Otsuka, M.; Ramos, M. J.. "A molecular modeling study of inhibitors of nuclear factor kappa-B (p50) - DNA binding". Journal of Computer-Aided Molecular Design 17 12 (2003): 825-836.
    10.1023/b:jcam.0000021835.72265.63
  386. Silva, P. J.; Fernandes, P. A.; Ramos, M. J.. "A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase". Theoretical Chemistry Accounts 110 5 (2003): 345-351.
    10.1007/s00214-003-0476-9
  387. Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "The reduction of ribonucleotides catalyzed by the enzyme ribonucleotide reductase". Theoretical Chemistry Accounts 108 6 (2002): 352-364.
    10.1007/s00214-002-0393-3
  388. Melo, A.; Ramos, M. J.. "Theoretical study of the amino acid interactions in the binding region of the trypsin-pancreatic trypsin inhibitor complex". Journal of Molecular Structure-Theochem 580 (2002): 251-262.
    10.1016/S0166-1280(01)00621-2
  389. Henriques, E. S.; Floriano, W. B.; Reuter, N.; Melo, A.; Brown, D.; Gomes, Janf; Maigret, B.; Nascimento, M. A. C.; Ramos, M. J.. "The search for a new model structure of beta-Factor XIIa". Journal of Computer-Aided Molecular Design 15 4 (2001): 309-322.
    10.1023/a:1011128521816
  390. Melo, A.; Puga, A. T.; Gentil, F.; Brito, N.; Alves, A. P.; Ramos, M. J.. "Byte structure variable length coding (BS-VLC): A new specific algorithm applied in the compression of trajectories generated by molecular dynamics". Journal of Chemical Information and Computer Sciences 40 3 (2000): 559-566.
    10.1021/ci990069u
  391. Magalhaes, AL; Maigret, B; Gomes, JANF; Ramos, MJ. "Hybrid QM/MM study of a fundamental biological interaction surrounded by its protein environment". INTERNET JOURNAL OF CHEMISTRY (2000):
  392. Magalhaes, A. L.; Madail, Srrs; Ramos, M. J.. "Prediction of the Raman spectrum of the aqueous formate anion by a combined density functional theory and self-consistent-reaction-field study". Theoretical Chemistry Accounts 105 1 (2000): 68-76.
    10.1007/s002140000187
  393. Melo, A.; Ramos, M. J.; Floriano, W. B.; Gomes, Janf; Leao, J. F. R.; Magalhaes, A. L.; Maigret, B.; Nascimento, M. C.; Reuter, N.. "Theoretical study of arginine-carboxylate interactions". Journal of Molecular Structure-Theochem 463 1-2 (1999): 81-90. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000079425800012&KeyUID=WOS:000079425800012.
    10.1016/s0166-1280(98)00396-0
  394. Melo, A.; Ramos, M. J.. "A new partitioning scheme for molecular interacting systems within a multiconfigurational or monoconfigurational Hartree-Fock formalism". International Journal of Quantum Chemistry 72 3 (1999): 157-176.
    10.1002/(sici)1097-461x(1999)72:3<157::aid-qua1>3.3.co;2-#
  395. Henriques, E. S.; Bastos, M.; Geraldes, Cfgc; Ramos, M. J.. "Computational approaches to the study of some lanthanide (III) - Polyazamacrocyclic chelates for magnetic resonance imaging". International Journal of Quantum Chemistry 73 2 (1999): 237-248.
    10.1002/(sici)1097-461x(1999)73:2<237::aid-qua17>3.3.co;2-n
  396. Ramos, M. J.; Melo, A.; Henriques, E. S.; Gomes, Janf; Reuter, N.; Maigret, B.; Floriano, W. B.; Nascimento, M. A. C.. "Modeling enzyme-inhibitor interactions in serine proteases". International Journal of Quantum Chemistry 74 3 (1999): 299-314.
    10.1002/(sici)1097-461x(1999)74:3<299::aid-qua3>3.0.co;2-k
  397. Henriques, E. F.; Ramos, M. J.; Reynolds, C. A.. "Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein". Journal of Computer-Aided Molecular Design 11 6 (1997): 547-556. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000071973800003&KeyUID=WOS:000071973800003.
    10.1023/a:1007919812771
  398. Bastos, M.; Afonso, M.; Cacote, M. H. M.; Ramos, M. J.. "Interactions in the model system alpha-cyclodextrin-glycerol - Experimental and theoretical study". Journal of the Chemical Society-Faraday Transactions 93 11 (1997): 2061-2067.
    10.1039/a608163k
  399. Melo, A.; Ramos, M. J.. "The nature of trypsin-pancreatic trypsin inhibitor binding: Free energy calculation of Tys(39)->Phe(39) mutation in trypsin". Journal of Peptide Research 50 5 (1997): 382-387. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:A1997YC65100009&KeyUID=WOS:A1997YC65100009.
  400. Melo, A.; Ramos, M. J.. "PROTON-TRANSFER IN ARGININE-CARBOXYLATE INTERACTIONS". Chemical Physics Letters 245 4-5 (1995): 498-502.
    10.1016/0009-2614(95)01058-H
  401. Ramos, M.J.; Richards, W.G.. "Computer models of beta-factor XIIa and inhibitor". Drug News and Perspectives 5 6 (1992): 325-330. http://www.scopus.com/inward/record.url?eid=2-s2.0-0026730608&partnerID=MN8TOARS.
  402. Ramos, M. J.. "MODEL STRUCTURE FOR THE HUMAN BLOOD-COAGULATION AGENT BETA-FACTOR XIIA". Journal of Molecular Graphics 9 2 (1991): 91-&.
    10.1016/0263-7855(91)85004-i
  403. Lopes de Magalhães, A; Ramos, MJ; Lopes de Magalhães, A.; Ramos, M.J.. "Calculation of hyperfine coupling constants of muonated radicals". Chemical Physics Letters 165 6 (1990): 528-534. https://www.authenticus.pt/P-00H-5S1.
    10.1016/0009-2614(90)87033-n
  404. RAMOS, MJ. "MUON CHEMISTRY AND MU-SR". JOURNAL DE CHIMIE PHYSIQUE ET DE PHYSICO-CHIMIE BIOLOGIQUE (1987): https://www.authenticus.pt/P-001-V7C.
  405. Webster, B.; Hilczer, M.; Ramos, M. J.; Carmichael, I.. "THE INCLUSION OF D-TYPE GAUSSIAN FUNCTIONS IN THE ANALYTIC METHOD FOR THE CALCULATION OF ELECTROSTATIC MOLECULAR POTENTIALS - INTERACTION OF A PROTON OR A POSITIVE MUON WITH CARBON-MONOXIDE". Journal of the Chemical Society-Faraday Transactions Ii 81 (1985): 1761-1769.
    10.1039/f29858101761
  406. Amaral, A.; Gomes, J.A.N.F.; Ramos, M.. "Preface". Journal of Molecular Structure: THEOCHEM 120 C (1985): http://www.scopus.com/inward/record.url?eid=2-s2.0-46549104257&partnerID=MN8TOARS.
  407. Ramos, M. J.; McKenna, D.; Webster, B. C.; Roduner, E.. "MUON SPIN ROTATION SPECTRA FOR MUONIUM ISOTOPICALLY SUBSTITUTED ETHYL RADICALS". Journal of the Chemical Society-Faraday Transactions I 80 (1984): 255-265.
    10.1039/F19848000255
  408. Ramos, M. J.; McKenna, D.; Webster, B. C.; Roduner, E.. "THE BARRIERS TO INTERNAL-ROTATION FOR MUONIC-SUBSTITUTED ETHYL RADICALS". Journal of the Chemical Society-Faraday Transactions I 80 (1984): 267-274.
    10.1039/F19848000267
  409. Ramos, M. J.; Webster, B.. "AN ANALYTIC METHOD FOR THE CALCULATION OF ELECTROSTATIC MOLECULAR POTENTIALS". Journal of the Chemical Society-Faraday Transactions Ii 79 (1983): 1389-1398.
    10.1039/f29837901389
  410. Roduner, E.; Strub, W.; Burkhard, P.; Hochmann, J.; Percival, P. W.; Fischer, H.; Ramos, M.; Webster, B. C.. "MUONIUM SUBSTITUTED ORGANIC FREE-RADICALS IN LIQUIDS - MUON ELECTRON HYPERFINE COUPLING-CONSTANTS OF ALKYL AND ALLYL RADICALS". Chemical Physics 67 3 (1982): 275-285.
    10.1016/0301-0104(82)85189-6

Other

Dataset
  1. Coimbra, João TS; Fernandes, Pedro Alexandrino; Ramos, Maria João. Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations". Zenodo. 2023.
    https://doi.org/10.5281/zenodo.8255787
Other output
  1. The chemistry of snake venom and its medicinal potential. 2022. Oliveira, AL; Viegas, MF; da Silva, SL; Soares, AM; Ramos, MJ; Fernandes, PA.
    10.1038/s41570-022-00393-7
  2. Lessons from a Single Amino Acid Substitution: Anticancer and Antibacterial Properties of Two Phospholipase A(2)-Derived Peptides. 2022. Almeida, JR; Mendes, B; Lancellotti, M; Franchi, GC; Passos, O; Ramos, MJ; Fernandes, PA; et al.
    10.3390/cimb44010004
  3. Novel Pet-Degrading Enzymes: Structure-Function from a Computational Perspective. 2021. Berselli, A; Ramos, MJ; Menziani, MC.
    10.1002/cbic.202000841
  4. Animal Fatty Acid Synthase: A Chemical Nanofactory. 2021. Paiva, P; Medina, FE; Viegas, M; Ferreira, P; Neves, RPP; Sousa, JPM; Ramos, MJ; Fernandes, PA.
    10.1021/acs.chemrev.1c00147
  5. Estrogen receptor-positive (ER+) breast cancer treatment: Are multi-target compounds the next promising approach?. 2020. Almeida, CF; Oliveira, A; Ramos, MJ; Fernandes, PA; Teixeira, N; Amaral, C.
    10.1016/j.bcp.2020.113989
  6. The bacterial 4S pathway - an economical alternative for crude oil desulphurization that reduces CO2 emissions. 2020. Sousa, JPM; Ferreira, P; Neves, RPP; Ramos, MJ; Fernandes, PA.
    10.1039/d0gc02055a
  7. Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins. 2019. Sousa, SF; Neves, RPP; Waheed, SO; Fernandes, PA; Ramos, MJ.
    10.1515/hsz-2018-0319
  8. Inside Cover: The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac (Chem. Eur. J. 37/2016). 2016. Brás, NF; Ferreira, P; Calixto, AR; Jaspars, M; Houssen, W; Naismith, JH; Fernandes, PA; Ramos, MJ.
    10.1002/chem.201603742
  9. Development of Ribonucleotide Reductase Inhibitor: A Review on Structure Activity Relationships. 2013. Moorthy, NSHN; Cerqueira, NMFSA; Ramos, MJ; Fernandes, PA. https://www.authenticus.pt/P-008-H9D.
    10.2174/13895575113136660090
  10. A DFT study of the applicability of the charge balance model in two-metal enzymes: The case of cAMP-dependent protein kinase (vol 571, pg 66, 2013). 2013. Ribeiro, AJM; Ramos, MJ; Fernandes, PA; Russo, N. https://www.authenticus.pt/P-006-92Y.
    10.1016/j.cplett.2013.06.024
  11. SPECIAL ISSUE - THEORETICAL CHEMISTRY 1984 - PROCEEDINGS OF THE 15TH CONGRESS OF THEORETICAL CHEMISTS OF LATIN EXPRESSION, VIANA-DO-CASTELO, PORTUGAL, 2-6 SEPTEMBER 1984. 1985. AMARAL, A; GOMES, JANF; RAMOS, MJ. https://www.authenticus.pt/P-005-6G3.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2020 PLENARIES/INVITED TALKS - I have been invited to deliver 120 Invited Talks / Plenaries in International Conferences. Details for 2020-1986 are given in www.fc.up.pt/pessoas/mjramos/PLENARIES_INVITED_TALKS.pdf

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2020 - Current SUPERVISION OF SCIENTIFIC RESEARCHERS - I supervise/have supervised 6 Senior Researchers (I.A.), 8 Post-Docs, 35 PhD. students, 21 M.Sc. students, 18 Research Grant Students (B.I.), 3 Research Initiation Grant Students (B.I.I.) and 58 last year Undergraduate Research Project Students (Chemistry and Biochemistry) - for more details on names please consult www.fc.up.pt/pessoas/mjramos/SUPERVISION_OF_SCIENTIFIC_RESEARCHERS.pdf
Supervisor

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2020 PARTICIPATION IN ACADEMIC JURIS - Details on International and national PhD juris are given in www.fc.up.pt/pessoas/mjramos/ACADEMIC_JURIS.pdf National and international cademic juris (PhD)

Consulting

Activity description Institution / Organization
1999 - 2020 RESEARCH INTERESTS - I am/have been a consultant for several companies and my research interests are given in more detail in www.fc.up.pt/pessoas/mjramos/RESEARCH_INTERESTS.pdf

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2000 - 2020 EVALUATION WORK - I have been an evaluator of research projects / university positions / universities, for many years now. Details for 2020-2000 are given in www.fc.up.pt/pessoas/mjramos/EVALUATION_WORK.pdf

Journal scientific committee

Journal title (ISSN) Publisher
2020 - Current REVIEWING - I have been a reviewer for many scientific journals. Details are given in www.fc.up.pt/pessoas/mjramos/REVIEWING.pdf
Distinctions

Award

2024 Chemistry Europe Fellow
2023 Excellence in Research Prize
Universidade do Porto, Portugal
2020 Centenario Prize
Universidade do Porto Faculdade de Ciências, Portugal
2019 Medinabeitia-Lourenço Prize
2014 Honorary Doctorate, Stockholm University, Sweden
2001 Italgas Prize for Research and Technological Innovation
1974 Best student
Fundação Calouste Gulbenkian, Portugal