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I have a BSc in Chemistry (1993) from the University of Porto and a Ph.D. in Chemistry (2000) from the same University. I am currently an Associate Professor at the University of Porto, where I teach computational biochemistry, bioinformatics, and drug discovery courses. I do research in the same field, having published more than 300 articles in peer-reviewed journals. My research focuses on studying the reaction mechanisms of enzymes with hybrid quantum/classical methods, in the modeling and simulation of complex enzymatic/proteomic systems, in the simulation of mutagenesis, and in drug discovery. The enzymatic systems I study generally have a therapeutic interest, for which drugs might be developed. I have recently focused on optimizing enzymes of industrial interest through rational mutagenesis and in the study of enzymatic and protein toxins from animal venoms.
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Identificação

Identificação pessoal

Nome completo
Pedro Manuel Azevedo Alexandrino Fernandes

Nomes de citação

  • Fernandes, Pedro Alexandrino

Identificadores de autor

Ciência ID
CF15-D864-2EE8
ORCID iD
0000-0003-2748-4722
Google Scholar ID
https://scholar.google.com/citations?user=iaO4X2kAAAAJ&hl=en
Researcher Id
D-6327-2013
Scopus Author Id
50062380800

Telefones

Telefone
  • 220402667 Ext.: 30667 (Profissional)

Moradas

  • LAQV- Departamento de Química e Bioquímica, Rua do Campo Alegre, S/N, 4169-007, Porto, Porto, Portugal (Profissional)

Websites

Domínios de atuação

  • Ciências Exatas - Química

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português (Idioma materno)
Francês Utilizador independente (B2) Utilizador proficiente (C2) Utilizador independente (B2) Utilizador proficiente (C2) Utilizador proficiente (C2)
Inglês Utilizador proficiente (C1) Utilizador proficiente (C2) Utilizador proficiente (C1) Utilizador proficiente (C2) Utilizador proficiente (C2)
Formação
Grau Classificação
2010/01/06 - 2010/01/07
Concluído
 Química (Título de Agregado)
Universidade do Porto Faculdade de Ciências, Portugal
 Unanimidade
2000/02/29
Concluído
 Doutoramento em Química (Doutoramento)
Especialização em Outra:Sem especialidade
Universidade do Porto, Portugal
"Reacções de Transferência Iónica Através da Interface Entre Líquidos Irriscíveis" (TESE/DISSERTAÇÃO)
 Unanimidade
1989 - 1993/09/06
Concluído
 Química (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal
 15
Percurso profissional

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento 		Empregador
2024/03/14 - Atual Professor Catedrático (Docente Universitário) Universidade do Porto Faculdade de Ciências, Portugal
Universidade do Porto Faculdade de Ciências, Portugal
2009/03/01 - 2024/03/14 Professor Associado (Docente Universitário) Universidade do Porto, Portugal
1999/12/01 - 2009/03/01 Professor Auxiliar Convidado (Docente Universitário) Universidade do Porto Faculdade de Ciências, Portugal
Projetos

Projeto

Designação Financiadores
2012/05/01 - Atual New drugs for hypertension
info:eu-repo/grantAgreement/FCT/COMPETE/121744/PT
Investigador
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2023/01/01 - 2028/12/31 Enzymatic Deconstruction of Thermoset Plastics
En’Zync – 0072891
Co-Investigador Responsável (Co-IR)
REQUIMTE LAQV Porto, Portugal
 Danmarks Tekniske Universitet The Novo Nordisk Foundation Center for Biosustainability
Em curso
2023/01 - 2028/12 Enzymatic Deconstruction of Thermoset Plastics
EnZync 0072891
 Danmarks Tekniske Universitet The Novo Nordisk Foundation Center for Biosustainability
2023/02/01 - 2026/01/31 Multi-target Teragnostics for the Alzheimer Disease
2022.06064.PTDC
Investigador
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2021/03/29 - 2024/03/28 Murderous Venom - Towards a Universal Antidote Against Snakebite
PTDC/QUI-OUT/1401/2020
Investigador responsável
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
2023/03/08 - 2024/03/07 Developing a Universal and Affordable Antidote for Snakebite
EHPC-REG-2022R03-20
Investigador responsável
REQUIMTE LAQV Porto, Portugal
 EuroHPC Joint Undertaking
2022/06/01 - 2023/05/31 The mechanism of action of the sPLA2-like toxin of viper venom.
2021.09753.CPCA
Investigador responsável
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2020 - 2023 2019215204-Biodegrading Plastics.
2019215204
Investigador
REQUIMTE LAQV Porto, Portugal

Universidade do Porto Departamento de Química e Bioquímica, Portugal
PRACE – Partnership for Advanced Computing in Europe
Em curso
2022/06/01 - 2022/08/31 An Universal and Affordable Antidote for Snakebite
EHPC-BEN-2022B05-080
Investigador responsável
REQUIMTE LAQV Porto, Portugal
 EuroHPC Joint Undertaking
Concluído
2020 - 2020 A drug discovery project against the main protease of Covid-19
COVID-19-49
Investigador
REQUIMTE LAQV Porto, Portugal

Universidade do Porto Departamento de Química e Bioquímica, Portugal
Partnership for Advanced Computing In Europe
Concluído
2020 - 2020 Drug discovery targeting Covid-19
XSEDE ASC200029
Investigador
Universidade do Porto Departamento de Química e Bioquímica, Portugal

REQUIMTE LAQV Porto, Portugal
Extreme Science and Engineering Discovery Environment- National Science Foundation
Concluído
2019 - 2020 Enzyme instantaneous disorder as a key player in the catalytic power of enzymes
CHM151-2019
Investigador responsável
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Oak Ridge National Laboratory
Em curso
2018 - 2020 New Biocatalysts for Green Crude Oil Desulfurization
PTDC/QUI-QFI/28714/2017
Investigador responsável
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2018 - 2020 Interdisciplinary in silico, organic synthesis, in vitro, and in vivo studies towards new anti-diabetic flavonoid scaffolds
PTDC/MED-QUI/29241/2017
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2015 - 2020 TCCM - Theoretical Chemistry and Computational Modelling
ITN-EJD-642294
Investigador
Universidade do Porto Faculdade de Ciências, Portugal
Concluído
2016 - 2019 (Fe)rrying plants to prevent chlorosis
PTDC/AGR-PRO/3515/2014
Investigador
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2016 - 2019 New Technologies for three Health Challenges of Modern Societies: Diabetes, Drug Abuse and Kidney Diseases
NORTE-01-0145-FEDER-000024
Investigador responsável
REQUIMTE LAQV Porto, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Concluído
2018 - 2018 Bacterial initiation factors and termination factors as new targets for novel antibiotics
PRACE 2018184467
Investigador
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal

Universidade do Porto Departamento de Química e Bioquímica, Portugal
Partnership for Advanced Computing In Europe
Concluído
2013/01/01 - 2018 ENZYMATIC CATALYSIS - seeking a global picture
info:eu-repo/grantAgreement/FCT/COMPETE/128544/PT
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2014 - 2015 Consensus Scoring – A new methodology to identify lead compounds for the pharmaceutical industry
EXPL/QEQ-COM/1125/2013
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2010 - 2012 Molecular Mechanisms of Hypercholesterolemia: New insights and New Therapeutic Strategies
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/102760/PT
Investigador responsável
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2010 - 2012 New Biomolecular Force Field
EXPL/QEQ-COM/1125/2013
 Fundação para a Ciência e a Tecnologia
2009/01/02 - 2011 Novel Key Molecular Architectures to Target Infection
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/67915/PT
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2008 - 2010 Evolution of Phenogenetic Changes: Genetic Study of the Variation of Development Genes in Vertebrates
19. PTDC/BIA-BDE/69144/2006
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2008 - 2010 The modulation of retinoic acid signalling pathways by environmental pollutants in teleosts
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/68106/PT
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2008 - 2010 Spectroscopic and Computational Studies on the Catalytic Mechanism of Nitrate Reductase.
PTDC/QUI/67052/2006
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
Concluído
2008 - 2010 A combined approach of X-ray crystallography, NMR and computational chemistry for the study of the molecular interactions that define the ligand specificity in cellulosomal carbohydrate-binding modules.
PTDC/QUI/68286/2006
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2008 - 2010 Drug design towards the HIV-1 virus.
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/68302/PT
Investigador responsável
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2005 - 2008 Enzymatic catalysis: mechanistic studies of cancer-related human enzymes
info:eu-repo/grantAgreement/FCT/POCI/61563/PT
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2004 - 2007 HPC Infrastructure for Computational Chemistry at the Associated Laboratory REQUIMTE
CONC-REEQ/1236/2001
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2004 - 2007 HPC Infrastructure for Computational Chemistry at the Associated Laboratory REQUIMTE
CONC-REEQ/1236/2001
 Fundação para a Ciência e a Tecnologia
2004 - 2005 Molecular Determinants of Ligand Specificity in the Family 11 Carbohydrate Binding Modules
ReqMol
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
Concluído
2000 - 2003 Inhibition Mechanisms of Radical Enzymes - A QM/MM Study
POCTI/35376/QUI/1999
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
Produções

Publicações

Artigo em conferência
  1. Fernandes, P.; Leite, I.T.; Teixeira, J.M.; Hierro-Rodríguez, A.; Araújo, J.P.; Guerreiro, A.. "Sensing with metallic nanowires". 2014.
    10.1117/12.2059765
  2. Leite, I.T.; Fernandes, P.; Hierro-Rodriguez, A.; Teixeira, J.M.; Jorge, P.A.S.; Guerreiro, A.. "Analysis of a fibre optic sensor design based on SPR in nanowire metamaterial films". 2014.
    10.1117/12.2059766
Artigo em revista
  1. Carlos F. M. Silva; Diana C. G. A. Pinto; Pedro A. Fernandes; Artur M. S. Silva. "Evolution of the Quinoline Scaffold for the Treatment of Leishmaniasis: A Structural Perspective". Pharmaceuticals (2024): https://doi.org/10.3390/ph17030285.
    10.3390/ph17030285
  2. Ana L. Novo de Oliveira; Miguel T. Lacerda; Maria J. Ramos; Pedro A. Fernandes. "Viper Venom Phospholipase A2 Database: The Structural and Functional Anatomy of a Primary Toxin in Envenomation". Toxins (2024): https://doi.org/10.3390/toxins16020071.
    10.3390/toxins16020071
  3. Carola Jerves; Rui P. P. Neves; Saulo L. da Silva; Maria J. Ramos; Pedro A. Fernandes. "Rate-enhancing PETase mutations determined through DFT/MM molecular dynamics simulations". New Journal of Chemistry (2024): https://doi.org/10.1039/D3NJ04204A.
    10.1039/D3NJ04204A
  4. 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
  5. Juliana Castro-Amorim; Ana Oliveira; Ashis K. Mukherjee; Maria J. Ramos; Pedro A. Fernandes. "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 (2023): https://doi.org/10.1021/acs.jcim.2c01156.
    10.1021/acs.jcim.2c01156
  6. João Sousa; Nuno Azevedo Oliveira; Pedro Alexandrino Fernandes. "Rational Engineering of (S)-Norcoclaurine Synthase for Efficient Benzylisoquinoline Alkaloids Biosynthesis". Molecules (2023): https://www.mdpi.com/1420-3049/28/11/4265.
    10.3390/molecules28114265
  7. Juliana Castro-Amorim; Ana Novo de Oliveira; Saulo Luís Da Silva; Andreimar M. Soares; Ashis K. Mukherjee; Maria João Ramos; Pedro A. Fernandes. "Catalytically Active Snake Venom PLA2 Enzymes: An Overview of Its Elusive Mechanisms of Reaction". Journal of Medicinal Chemistry (2023): https://doi.org/10.1021/acs.jmedchem.3c00097.
    10.1021/acs.jmedchem.3c00097
  8. Rui P. P. Neves; Bruno Araújo; Maria J. Ramos; Pedro A. Fernandes. "Feedback Inhibition of DszC, a Crucial Enzyme for Crude Oil Biodessulfurization". Catalysts (2023): https://doi.org/10.3390/catal13040736.
    10.3390/catal13040736
  9. Carlos F. M. Silva; Teresa Leão; Filipa Dias; Ana M. Tomás; Diana C. G. A. Pinto; Eduardo F. T. Oliveira; Ana Oliveira; Pedro A. Fernandes; Artur M. S. Silva. "Structure–Activity Relationship Studies of 9-Alkylamino-1,2,3,4-tetrahydroacridines against Leishmania (Leishmania) infantum Promastigotes". Pharmaceutics (2023): https://doi.org/10.3390/pharmaceutics15020669.
    10.3390/pharmaceutics15020669
  10. Alexandre V. Pinto; Pedro Ferreira; Pedro A. Fernandes; Alexandre L. Magalhães; Maria J. Ramos. "Development of Nanoscale Graphene Oxide Models for the Adsorption of Biological Molecules". The Journal of Physical Chemistry B (2023): https://doi.org/10.1021/acs.jpcb.2c06037.
    10.1021/acs.jpcb.2c06037
  11. Rui P. P. Neves; Maria J. Ramos; Pedro A. Fernandes. "Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis". Journal of Chemical Information and Modeling (2023): https://doi.org/10.1021/acs.jcim.2c01337.
    10.1021/acs.jcim.2c01337
  12. Ong, How Chee; Coimbra, João T. S.; Ramos, Maria Joao Joao; Xing, Bengang; Fernandes, Pedro Alexandrino; García, Felipe. "Beyond the TPP+ “gold standard”: A new generation mitochondrial delivery vector based on extended PN frameworks.". Chemical Science (2023): http://dx.doi.org/10.1039/d2sc06508h.
    10.1039/d2sc06508h
  13. How Chee Ong; João T. S. Coimbra; Maria J. Ramos; Bengang Xing; Pedro A. Fernandes; Felipe García. "Beyond the TPP+ “gold standard”: a new generation mitochondrial delivery vector based on extended PN frameworks". Chemical Science (2023): https://doi.org/10.1039/D2SC06508H.
    10.1039/D2SC06508H
  14. Matilde F. Viegas; Rui P. P. Neves; Maria J. Ramos; Pedro A. Fernandes. "QM/MM Study of the Reaction Mechanism of Thermophilic Glucuronoyl Esterase for Biomass Treatment". ChemPhysChem (2022): https://doi.org/10.1002/cphc.202200269.
    10.1002/cphc.202200269
  15. Rui P. P. Neves; Pedro A. Fernandes; Maria J. Ramos. "Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by a-Amylase Explored with QM/MM Molecular Dynamics". Journal of Chemical Information and Modeling (2022): https://doi.org/10.1021/acs.jcim.2c00691.
    10.1021/acs.jcim.2c00691
  16. 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
  17. João T. S. Coimbra; Rui P. P. Neves; Ana V. Cunha; Maria J. Ramos; Pedro A. Fernandes. "Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease". Chemistry – A European Journal (2022): https://doi.org/10.1002/chem.202201066.
    10.1002/chem.202201066
  18. Rui P. P. Neves; Ana V. Cunha; Pedro A. Fernandes; Maria J. Ramos. "Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms". ChemPhysChem 23 13 (2022): https://doi.org/10.1002/cphc.202200159.
    10.1002/cphc.202200159
  19. Ana L. Oliveira; Matilde F. Viegas; Saulo L. da Silva; Andreimar M. Soares; Maria J. Ramos; Pedro A. Fernandes. "The chemistry of snake venom and its medicinal potential". Nature Reviews Chemistry (2022): https://doi.org/10.1038/s41570-022-00393-7.
    10.1038/s41570-022-00393-7
  20. Luís M. C. Teixeira; João T. S. Coimbra; Maria João Ramos; Pedro Alexandrino Fernandes. "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): https://doi.org/10.1021/acs.jcim.1c01561.
    10.1021/acs.jcim.1c01561
  21. Pedro A. Fernandes; Óscar Passos; Maria J. Ramos. "Necessity is the Mother of Invention: A Remote Molecular Bioinformatics Practical Course in the COVID-19 Era". Journal of Chemical Education (2022): https://doi.org/10.1021/acs.jchemed.1c01195.
    10.1021/acs.jchemed.1c01195
  22. "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 (BBA) - Biomembranes 1864 3 (2022): 183838-183838. http://dx.doi.org/10.1016/j.bbamem.2021.183838.
    10.1016/j.bbamem.2021.183838
  23. "The archaeal non-heme iron-containing Sulfur Oxygenase Reductase". Coordination Chemistry Reviews 455 (2022): 214358-214358. http://dx.doi.org/10.1016/j.ccr.2021.214358.
    10.1016/j.ccr.2021.214358
  24. "Engineering of PKS Megaenzymes—A Promising Way to Biosynthesize High-Value Active Molecules". Topics in Catalysis 65 1-4 (2022): 544-562. http://dx.doi.org/10.1007/s11244-021-01490-5.
    10.1007/s11244-021-01490-5
  25. Carlos F. M. Silva; Diana C. G. A. Pinto; Pedro A. Fernandes; Artur M. S. Silva. "Evolution of Acridines and Xanthenes as a Core Structure for the Development of Antileishmanial Agents". Pharmaceuticals (2022): https://doi.org/10.3390/ph15020148.
    10.3390/ph15020148
  26. João P. M. Sousa; Maria J. Ramos; Pedro A. Fernandes. "Modern Strategies for the Diversification of the Supply of Natural Compounds: The Case of Alkaloid Painkillers". ChemBioChem (2022): https://doi.org/10.1002/cbic.202100623.
    10.1002/cbic.202100623
  27. Carina Proença; Ana T. Rufino; José Miguel P. Ferreira de Oliveira; Marisa Freitas; Pedro A. Fernandes; Artur M. S. Silva; Eduarda Fernandes. "Inhibitory activity of flavonoids against human sucrase-isomaltase (a-glucosidase) activity in a Caco-2/TC7 cellular model". Food & Function (2022): https://doi.org/10.1039/D1FO02995A.
    10.1039/D1FO02995A
  28. Anna Cebrián-Prats; Alexandre Pinto; Àngels González-Lafont; Pedro A. Fernandes; José M. Lluch. "The role of acetylated cyclooxygenase-2 in the biosynthesis of resolvin precursors derived from eicosapentaenoic acid". Organic & Biomolecular Chemistry (2022): https://doi.org/10.1039/D1OB01932E.
    10.1039/D1OB01932E
  29. João Marques Sousa; Matilde Ribeiro Viegas; Pedro Teixeira Ferreira; Pedro Coelho Paiva; Ana Luísa Oliveira; Pedro Alexandrino Fernandes; Maria João Ramos. "MOLECULAR BIOINFORMATICS". Revista de Ciência Elementar 9 4 (2021): https://doi.org/10.24927/rce2021.075.
    10.24927/rce2021.075
  30. Pedro Fernandes; Francisco Félix. "“Tão natural”". Revista de Ciência Elementar (2021): https://doi.org/10.24927/rce2021.072.
    10.24927/rce2021.072
  31. "Lessons from a Single Amino Acid Substitution: Anticancer and Antibacterial Properties of Two Phospholipase A2-Derived Peptides". Current Issues in Molecular Biology 44 1 (2021): 46-62. http://dx.doi.org/10.3390/cimb44010004.
    10.3390/cimb44010004
  32. Upasana Puzari; Pedro Alexandrino Fernandes; Ashis K. Mukherjee. "Advances in the Therapeutic Application of Small-Molecule Inhibitors and Repurposed Drugs against Snakebite". Journal of Medicinal Chemistry 64 19 (2021): 13938-13979. https://doi.org/10.1021/acs.jmedchem.1c00266.
    10.1021/acs.jmedchem.1c00266
  33. "The Catalytic Mechanism of the Retaining Glycosyltransferase Mannosylglycerate Synthase". Chemistry – A European Journal 27 56 (2021): 13998-14006. http://dx.doi.org/10.1002/chem.202101724.
    10.1002/chem.202101724
  34. Carola Jerves; Rui P. P. Neves; Maria J. Ramos; Saulo da Silva; Pedro A. Fernandes. "Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations". ACS Catalysis (2021): https://doi.org/10.1021/acscatal.1c03700.
    10.1021/acscatal.1c03700
  35. Alexandre V. Pinto; Pedro Ferreira; Rui P. P. Neves; Pedro A. Fernandes; Maria J. Ramos; Alexandre L. Magalhães. "Reaction Mechanism of MHETase, a PET Degrading Enzyme". ACS Catalysis (2021): 10416-10428. https://doi.org/10.1021/acscatal.1c02444.
    10.1021/acscatal.1c02444
  36. Pedro Paiva; Fabiola E. Medina; Matilde Viegas; Pedro Ferreira; Rui P. P. Neves; João P. M. Sousa; Maria J. Ramos; Pedro A. Fernandes. "Animal Fatty Acid Synthase: A Chemical Nanofactory". Chemical Reviews (2021): https://doi.org/10.1021/acs.chemrev.1c00147.
    10.1021/acs.chemrev.1c00147
  37. Matilde Viegas; Maria João Ramos; Pedro Alexandrino Fernandes. "Thermophilic Enzymes". U.Porto Journal of Engineering (2021): https://doi.org/10.24840/2183-6493_007.003_0002.
    10.24840/2183-6493_007.003_0002
  38. "Chromeno[3,4-b]xanthones as First-in-Class AChE and Aß Aggregation Dual-Inhibitors". International Journal of Molecular Sciences 22 8 (2021): 4145-4145. http://dx.doi.org/10.3390/ijms22084145.
    10.3390/ijms22084145
  39. "Passive Diffusion of Ciprofloxacin and its Metalloantibiotic: A Computational and Experimental study". Journal of Molecular Biology 433 9 (2021): 166911-166911. http://dx.doi.org/10.1016/j.jmb.2021.166911.
    10.1016/j.jmb.2021.166911
  40. João T. S. Coimbra; Ralph Feghali; Rui P. Ribeiro; Maria J. Ramos; Pedro A. Fernandes; Coimbra, J.T.S.; Feghali, R.; et al. "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. https://doi.org/10.1039/D0RA09995C.
    10.1039/D0RA09995C
  41. Almeida, C.F.; Teixeira, N.; Oliveira, A.; Augusto, T.V.; Correia-da-Silva, G.; Ramos, M.J.; Fernandes, P.A.; Amaral, C.. "Discovery of a multi-target compound for estrogen receptor-positive (ER+) breast cancer: Involvement of aromatase and ERs". Biochimie 181 (2021): 65-76. http://www.scopus.com/inward/record.url?eid=2-s2.0-85097475676&partnerID=MN8TOARS.
    10.1016/j.biochi.2020.11.023
  42. Resende, L.M.; Almeida, J.R.; Guaraca-Medina, T.A.; Viegas, M.F.; Soares, A.M.; Ramos, M.J.; Fernandes, P.A.; Marangoni, S.; Da Silva, S.L.. "Structural, enzymatic and pharmacological profiles of AplTX-II - A basic sPLA2 (D49) isolated from the Agkistrodon piscivorus leucostoma snake venom". International Journal of Biological Macromolecules 175 (2021): 572-585. http://www.scopus.com/inward/record.url?eid=2-s2.0-85100730003&partnerID=MN8TOARS.
    10.1016/j.ijbiomac.2021.01.187
  43. Brás, N.F.; Ferreira, P.; Calixto, A.R.; Jaspars, M.; Houssen, W.; Naismith, J.H.; Fernandes, P.A.; Ramos, M.J.. "Corrigendum: The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac (Chemistry - A European Journal, (2016), 22, 37, (13089-13097), 10.1002/chem.201601670)". Chemistry - A European Journal (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85099750694&partnerID=MN8TOARS.
    10.1002/chem.202100062
  44. Jordi Soler; Pedro Paiva; Maria J. Ramos; Pedro A. Fernandes; Marie Brut. "Unraveling the cGAS catalytic mechanism upon DNA activation through molecular dynamics simulations". Physical Chemistry Chemical Physics (2021): https://doi.org/10.1039/D1CP00378J.
    10.1039/D1CP00378J
  45. How Chee Ong; João T. S. Coimbra; Germain Kwek; Maria J. Ramos; Bengang Xing; Pedro A. Fernandes; Felipe García. "Alkyl vs. aryl modifications: a comparative study on modular modifications of triphenylphosphonium mitochondrial vectors". RSC Chemical Biology (2021): https://doi.org/10.1039/D1CB00099C.
    10.1039/D1CB00099C
  46. Carlos F. M. Silva; Diana C. G. A. Pinto; Pedro A. Fernandes; Artur M. S. Silva. "Evolution of chromone-like compounds as potential antileishmanial agents, through the 21st century". Expert Opinion on Drug Discovery (2020): 1-15. https://doi.org/10.1080/17460441.2020.1801630.
    10.1080/17460441.2020.1801630
  47. Kenneth Goossens; Rui PP Neves; Pedro A Fernandes; Hans De Winter. "A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes". Journal of Chemical Information and Modeling (2020): https://doi.org/10.1021/acs.jcim.0c00377.
    10.1021/acs.jcim.0c00377
  48. Pedro Paiva; Maria J. Ramos; Pedro A. Fernandes. "Assessing the validity of DLPNO-CCSD (T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions". Journal of Computational Chemistry (2020): https://doi.org/10.1002/jcc.26401.
    10.1002/jcc.26401
  49. Pedro Ferreira; Nuno M. F. Sousa A. Cerqueira; Pedro Alexandrino Fernandes; Maria João Romão; Maria João Ramos. "Catalytic Mechanism of Human Aldehyde Oxidase". ACS Catalysis (2020): 9276-9286. https://doi.org/10.1021/acscatal.0c02627.
    10.1021/acscatal.0c02627
  50. João P. M. Sousa; Rui P. P. Neves; Sérgio F. Sousa; Maria J. Ramos; Pedro A. Fernandes. "Reaction Mechanism and Determinants for Efficient Catalysis by DszB, a Key Enzyme for Crude Oil Bio-desulfurization". ACS Catalysis (2020): 9545-9554. https://doi.org/10.1021/acscatal.0c03122.
    10.1021/acscatal.0c03122
  51. Fernandes, Pedro Alexandrino. "Activation free energy, substrate binding free energy and enzyme efficiency fall in a very narrow range of values for most enzymes". ACS Catalysis (2020): https://pubs.acs.org/doi/10.1021/acscatal.0c01947.
    10.1021/acscatal.0c01947
  52. Pedro Fernandes; Maria João Ramos. "O sabão contra a COVID-19". Revista de Ciência Elementar 8 2 (2020): https://doi.org/10.24927/rce2020.019.
    10.24927/rce2020.019
  53. Pedro Fernandes; Maria João Ramos. "O álcool contra a COVID-19". Revista de Ciência Elementar 8 2 (2020): https://doi.org/10.24927/rce2020.018.
    10.24927/rce2020.018
  54. Pedro Fernandes. "A Ciência é a única arma". Revista de Ciência Elementar (2020): https://doi.org/10.24927/rce2020.017.
    10.24927/rce2020.017
  55. Carina Proença; Ana Oliveira; Marisa Freitas; Daniela Ribeiro; Joana L. C. Sousa; Maria J. Ramos; Artur M. S. Silva; Pedro A. Fernandes; Eduarda Fernandes. "Structural Specificity of Flavonoids in the Inhibition of Human Fructose 1,6-Bisphosphatase". Journal of Natural Products (2020): https://doi.org/10.1021/acs.jnatprod.0c00014.
    10.1021/acs.jnatprod.0c00014
  56. Mario Prejano; Fabiola E. Medina; Maria J. Ramos; Nino Russo; Pedro A. Fernandes; Tiziana Marino. "Correction to “How the Destabilization of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase”". ACS Catalysis (2020): 5372-5372. https://doi.org/10.1021/acscatal.0c01697.
    10.1021/acscatal.0c01697
  57. Fernandes, Pedro Alexandrino. "Cannabidiol (CBD) but not tetrahydrocannabinol (THC) dysregulate in vitro decidualization of human endometrial stromal cells by disruption of estrogen signaling". Reproductive Toxicology (2020): http://dx.doi.org/10.1016/j.reprotox.2020.01.003.
    10.1016/j.reprotox.2020.01.003
  58. Mario Prejanò; Fabiola E. Medina; Maria J. Ramos; Nino Russo; Pedro A. Fernandes; Tiziana Marino. "How the Destabilization of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase". ACS Catalysis (2020): https://doi.org/10.1021/acscatal.9b04690.
    10.1021/acscatal.9b04690
  59. Sousa, R.; Moorthy, N.S.H.N.; Fernandes, P.A.; Ramos, M.J.; Brás, N.F.. "Binding mode prediction and identification of new lead compounds from natural products as 3-OST enzyme inhibitors". Letters in Drug Design and Discovery 17 9 (2020): 1186-1196. http://www.scopus.com/inward/record.url?eid=2-s2.0-85090677162&partnerID=MN8TOARS.
    10.2174/1570180817666200313105944
  60. Ferreira Almeida, C.; Oliveira, A.; João Ramos, M.; Fernandes, P.A.; Teixeira, N.; Amaral, C.. "Estrogen receptor-positive (ER+) breast cancer treatment: Are multi-target compounds the next promising approach?". Biochemical Pharmacology 177 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85084205378&partnerID=MN8TOARS.
    10.1016/j.bcp.2020.113989
  61. Sousa, J.P.M.; Ferreira, P.; Neves, R.P.P.; Ramos, M.J.; Fernandes, P.A.. "The bacterial 4S pathway-an economical alternative for crude oil desulphurization that r educes CO2emissions". Green Chemistry 22 22 (2020): 7604-7621. http://www.scopus.com/inward/record.url?eid=2-s2.0-85096760072&partnerID=MN8TOARS.
    10.1039/d0gc02055a
  62. Pedro Fernandes. "Fraudes e falsificações na Arte e Arqueologia desmascaradas pela datação por Carbono 14". Revista de Ciência Elementar 7 4 (2019): https://doi.org/10.24927/rce2019.072.
    10.24927/rce2019.072
  63. Fernandes, Pedro. "The Catalytic Mechanism of Human Transketolase". ChemPhysChem (2019): http://dx.doi.org/10.1002/cphc.201900650.
    10.1002/cphc.201900650
  64. Fernandes, Pedro. "Human Fatty Acid Synthase: A Computational Study of the Transfer of the Acyl Moieties from MAT to the ACP Domain". ChemCatChem (2019): http://dx.doi.org/10.1002/cctc.201900548.
    10.1002/cctc.201900548
  65. Fernandes, Pedro. "Anandamide targets aromatase: A breakthrough on human decidualization". Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids (2019): http://dx.doi.org/10.1016/j.bbalip.2019.08.008.
    10.1016/j.bbalip.2019.08.008
  66. Fernandes, Pedro. "Glutamine synthetase structure-catalysis relationship—Recent advances and applications". Wiley Interdisciplinary Reviews: Computational Molecular Science (2019): http://dx.doi.org/10.1002/wcms.1399.
    10.1002/wcms.1399
  67. Fernandes, Pedro. "Enabling Mitochondrial Uptake of Lipophilic Dications Using Methylated Triphenylphosphonium Moieties". Inorganic Chemistry (2019): http://dx.doi.org/10.1021/acs.inorgchem.8b03380.
    10.1021/acs.inorgchem.8b03380
  68. Fernandes, Pedro. "Benchmark of Density Functionals for the Calculation of the Redox Potential of Fe3+/Fe2+ Within Protein Coordination Shells". Frontiers in Chemistry (2019): http://dx.doi.org/10.3389/fchem.2019.00391.
    10.3389/fchem.2019.00391
  69. Fernandes, Pedro. "A computational study on the redox properties and binding affinities of iron complexes of hydroxypyridinones". Journal of Molecular Modeling (2019): http://dx.doi.org/10.1007/s00894-019-4037-0.
    10.1007/s00894-019-4037-0
  70. Fernandes, Pedro. "Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins". Biological Chemistry (2019): http://dx.doi.org/10.1515/hsz-2018-0319.
    10.1515/hsz-2018-0319
  71. Carina Proença; Marisa Freitas; Daniela Ribeiro; Sara M. Tomé; Eduardo F. T. Oliveira; Matilde F. Viegas; Alberto N. Araújo; et al. "Evaluation of a flavonoids library for inhibition of pancreatic a-amylase towards a structure–activity relationship". Journal of Enzyme Inhibition and Medicinal Chemistry (2019): https://doi.org/10.1080/14756366.2018.1558221.
    10.1080/14756366.2018.1558221
  72. 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
  73. 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.
  74. Ana Rita Calixto; Maria João Ramos; Pedro Alexandrino Fernandes; Calixto, A.R.; Ramos, M.J.; Fernandes, P.A.. "Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway". Chemical Science 10 30 (2019): 7212-7221. https://doi.org/10.1039/C9SC01464K.
    10.1039/C9SC01464K
  75. Carina Proença; Marisa Freitas; Daniela Ribeiro; Sara M. Tomé; Alberto N. Araújo; Artur M. S. Silva; Pedro A. Fernandes; et al. "The dipeptidyl peptidase-4 inhibitory effect of flavonoids is hindered in protein rich environments". Food & Function 10 9 (2019): 5718-5731. https://doi.org/10.1039/C9FO00722A.
    10.1039/C9FO00722A
  76. Medina, F.E.; Ramos, M.J.; Fernandes, P.A.. "Complexities of the Reaction Mechanisms of CC Double Bond Reduction in Mammalian Fatty Acid Synthase Studied with Quantum Mechanics/Molecular Mechanics Calculations". ACS Catalysis 9 12 (2019): 11404-11412. http://www.scopus.com/inward/record.url?eid=2-s2.0-85075061675&partnerID=MN8TOARS.
    10.1021/acscatal.9b03531
  77. Ferreira, P.; Cerqueira, N.M.F.S.A.; Coelho, C.; Fernandes, P.A.; Romão, M.J.; Ramos, M.J.; P. Ferreira; et al. "New insights about the monomer and homodimer structures of the human AOX1". Physical Chemistry Chemical Physics 21 25 (2019): 13545-13554. http://www.scopus.com/inward/record.url?eid=2-s2.0-85068418264&partnerID=MN8TOARS.
    10.1039/c9cp01040h
  78. Matilde Viegas; Maria João Ramos; Pedro Fernandes. "Biocombustíveis, serão a solução?". Revista de Ciência Elementar (2018): https://doi.org/10.24927/rce2018.043.
    10.24927/rce2018.043
  79. 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
  80. Proenca, C.; Freitas, M.; Ribeiro, D.; Sousa, J. L. C.; Carvalho, F.; Silva, A. M. S.; Fernandes, P. A.; Fernandes, E.. "Inhibition of protein tyrosine phosphatase 1B by flavonoids: A structure activity relationship study". Food and Chemical Toxicology 111 (2018): 474-481. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000423248100042&KeyUID=WOS:000423248100042.
    10.1016/j.fct.2017.11.039
  81. Jana, G. A.; Mendoza, F.; Osorio, M. I.; Alderete, J. B.; Fernandes, P. A.; Ramos, M. J.; Jimenez, V. A.. "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. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000429204000010&KeyUID=WOS:000429204000010.
    10.1039/c8ob00284c
  82. 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
  83. 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
  84. 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): 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
  85. 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
  86. 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
  87. 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
  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. 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
  90. 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
  91. 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
  92. 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
  93. 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
  94. 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
  95. 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
  96. Simoes, I. C. M.; Coimbra, J. T. S.; Neves, R. P. P.; Costa, I. P. D.; Ramos, M. J.; Fernandes, P. A.; Inês C. M. Simões; et al. "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
  97. 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
  98. Medina, F. E.; Neves, R. P. P.; Ramos, M. J.; Fernandes, P. A.; 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
  99. Pedro Fernandes; Ana Calixto. "Moléculas magníficas". Revista de Ciência Elementar 5 2 (2017): https://doi.org/10.24927%2Frce2017.027.
    10.24927/rce2017.027
  100. 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
  101. Ferreira, P.; Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives". Chemistry-a European Journal 23 68 (2017): 17231-17241. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000419670200001&KeyUID=WOS:000419670200001.
    10.1002/chem.201704057
  102. 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.
  103. Ribeiro, R. P.; Coimbra, J. T. S.; Ramos, M. J.; Fernandes, P. 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
  104. 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
  105. Barra, P. A.; Ribeiro, A. J. M.; Ramos, M. J.; Jimenez, V. A.; Alderete, J. B.; Fernandes, P. 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
  106. 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): 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
  107. Sousa, S. F.; Ribeiro, A. J. M.; Neves, R. P. P.; Bras, N. F.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "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
  108. Hu, Z.; Sim, Y.; Kon, O. L.; Ng, W. H.; Ribeiro, A. J. M.; Ramos, M. J.; Fernandes, P. 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
  109. Cerqueira, Nmfsa; 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
  110. Coimbra, J. T. S.; Fernandes, P. A.; Ramos, M. 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
  111. Simoes, I. C. M.; Costa, I. P. D.; Coimbra, J. T. S.; Ramos, M. J.; Fernandes, P. 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
  112. 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): 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
  113. Neves, R. P. P.; Fernandes, P. A.; Ramos, M. J.. "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
  114. Fernandes, H. S.; Teixeira, C. S. S.; Fernandes, P. A.; Ramos, M. J.; Cerqueira, Nmfsa. "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=WOS_CPL&KeyUT=WOS:000395130200005&KeyUID=WOS:000395130200005.
    10.1080/13543776.2017.1254194
  115. Medina, F. E.; Neves, R. P. P.; Ramos, M. J.; Fernandes, P. 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
  116. Proença, C.; Freitas, M.; Ribeiro, D.; Oliveira, E.F.T.; Sousa, J.L.C.; Tomé, S.M.; Ramos, M.J.; et al. "a-Glucosidase inhibition by flavonoids: an in vitro and in silico structure–activity relationship study". Journal of Enzyme Inhibition and Medicinal Chemistry 32 1 (2017): 1216-1228. http://www.scopus.com/inward/record.url?eid=2-s2.0-85029757909&partnerID=MN8TOARS.
    10.1080/14756366.2017.1368503
  117. Sousa, C.F.; Coimbra, J.T.S.; Gomes, I.; Franco, R.; Fernandes, P.A.; Gameiro, P.; Sousa, C. F.; Coimbra, J. T. S.; Fernandes, P. A.. "The binding of free and copper-complexed fluoroquinolones to OmpF porins: an experimental and molecular docking study". RSC Advances 7 17 (2017): 10009-10019. http://www.scopus.com/inward/record.url?eid=2-s2.0-85012008929&partnerID=MN8TOARS.
    10.1039/C6RA26466B
  118. Moorthy, Nshn; Sousa, S. F.; Ramos, M. J.; Fernandes, P. 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
  119. Cerqueira, Nmfsa; Oliveira, E. F.; Gesto, D. S.; Santos-Martins, D.; Moreira, C.; Moorthy, H. N.; Ramos, M. 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
  120. Moreira, C.; Ramos, M. J.; Fernandes, P. 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
  121. Oliveira, E. F.; Cerqueira, Nmfsa; Ramos, M. J.; Fernandes, P. 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
  122. Moreira, C.; Ramos, M. J.; Fernandes, P. A.. "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
  123. Llinas, P.; Chenon, M.; Nguyen, T. Q.; Moreira, C.; de Regibus, A.; Coquard, A.; Ramos, M. 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
  124. 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
  125. Oliveira, E. F.; Santos-Martins, D.; Ribeiro, A. M.; Bras, N. F.; Cerqueira, N. S.; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "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
  126. Sousa, S. F.; Sousa, J. F. M.; Barbosa, A. C. C.; Ferreira, C. E.; Neves, R. P. P.; Ribeiro, A. J. M.; Fernandes, P. A.; Ramos, M. J.. "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
  127. Sousa, R. P.; Fernandes, P. A.; Ramos, M. J.; Bras, N. 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
  128. Moorthy, Nshn; Sousa, S. F.; Ramos, M. J.; Fernandes, P. 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
  129. Bras, N. F.; Ferreira, P.; Calixto, A. R.; Jaspars, M.; Houssen, W.; Naismith, J. H.; Fernandes, P. A.; Ramos, M. 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
  130. Neves, R. P. P.; Fernandes, P. A.; Ramos, M. 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
  131. Santos-Martins, D.; Fernandes, P. A.; Ramos, M. J.. "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
  132. Brás, N.F.; Ferreira, P.; Calixto, A.R.; Jaspars, M.; Houssen, W.; Naismith, J.H.; Fernandes, P.A.; Ramos, M.J.. "Inside Cover: The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac (Chem. Eur. J. 37/2016)". Chemistry - A European Journal 22 37 (2016): 12946-12946. http://www.scopus.com/inward/record.url?eid=2-s2.0-84984941908&partnerID=MN8TOARS.
    10.1002/chem.201603742
  133. Pedro Fernandes. "Prémio Casa das Ciências". Revista de Ciência Elementar 3 3 (2015): https://doi.org/10.24927/rce2015.037.
    10.24927/rce2015.037
  134. Pedro Fernandes. "Casa das Ci¿ncias: Futuro Incerto?". Revista de Ciência Elementar 3 1 (2015): https://doi.org/10.24927/rce2015.001.
    10.24927/rce2015.001
  135. Pinto, Gaspar P.; Bras, Natercia F.; Perez, Marta A. S.; Fernandes, Pedro A.; Russo, Nino; Ramos, Maria J.; Toscano, Marirosa. "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
  136. Ribeiro, Antonio J. M.; Yang, Lifeng; Ramos, Maria J.; Fernandes, Pedro A.; Liang, Zhao-Xun; Hirao, Hajime. "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
  137. Cerqueira, Nuno M. F. S. A.; Coelho, Catarina; Bras, Natercia F.; Fernandes, Pedro A.; Garattini, Enrico; Terao, Mineko; Romao, Maria Joao; Ramos, Maria Joao. "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
  138. Moorthy, N. S. Hari Narayana; Cerqueira, Nuno M. F. S. A.; Ramos, Maria J.; Fernandes, Pedro 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
  139. Moreira, Irina S.; Martins, Joao M.; Coimbra, Joa T. S.; Ramos, Maria J.; Fernandes, Pedro 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
  140. Ribeiro, Antonio J. M.; Santos-Martins, Diogo; Russo, Nino; Rarnos, Maria J.; Fernandes, Pedro 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
  141. 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
  142. Shi, Yan X.; Liang, Rong Z.; Martin, Katherine A.; Weston, Nicholas; Gonzalez-Calera, Silvia; Ganguly, Rakesh; Li, Yongxin; 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
  143. 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
  144. 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
  145. Cerqueira, Nuno M. F. S. A.; Gesto, Diana; Oliveira, Eduardo F.; Santos-Martins, Diogo; Bras, Natercia F.; Sousa, Sergio F.; Fernandes, Pedro A.; Ramos, Maria 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
  146. Pedro Fernandes. "II Encontro Casa das Ciências". Revista de Ciência Elementar 2 3 (2014): https://doi.org/10.24927/rce2014.051.
    10.24927/rce2014.051
  147. 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 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84924860022&partnerID=MN8TOARS.
    10.1016/j.abb.2015.03.002
  148. Moreira, I.S.; Ramos, R.M.; Martins, J.M.; Fernandes, P.A.; Ramos, M.J.. "Are hot-spots occluded from water?". Journal of Biomolecular Structure and Dynamics 32 2 (2014): 186-197. http://www.scopus.com/inward/record.url?eid=2-s2.0-84889633435&partnerID=MN8TOARS.
    10.1080/07391102.2012.758598
  149. Ngo, H.-P.-T.; Cerqueira, N.M.F.S.A.; 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 2 (2014): 596-606. http://www.scopus.com/inward/record.url?eid=2-s2.0-84894146310&partnerID=MN8TOARS.
    10.1107/S1399004713031283
  150. Aranda, J.; Cerqueira, N.M.; Fernandes, P.A.; Roca, M.; Tuñon, I.; Ramos, M.J.. "The catalytic mechanism of carboxylesterases: a computational study.". Biochemistry 53 36 (2014): 5820-5829. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908352478&partnerID=MN8TOARS.
    10.1021/bi500934j
  151. 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
  152. Dourado, D.F.A.R.; Fernandes, P.A.; Mannervik, B.; Ramos, M.J.. "Isomerization of ¿5-androstene-3,17-dione into ¿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://www.scopus.com/inward/record.url?eid=2-s2.0-84905718002&partnerID=MN8TOARS.
    10.1021/jp410810q
  153. Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics studies on both bound and unbound renin protease". Journal of Biomolecular Structure and Dynamics 32 3 (2014): 351-363. http://www.scopus.com/inward/record.url?eid=2-s2.0-84892981145&partnerID=MN8TOARS.
    10.1080/07391102.2013.768553
  154. Silva, A.M.N.; Sousa, P.R.H.; Coimbra, J.T.S.; Brás, 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 1 (2014): 33-42. http://www.scopus.com/inward/record.url?eid=2-s2.0-84902345071&partnerID=MN8TOARS.
    10.1042/BJ20140133
  155. 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://www.scopus.com/inward/record.url?eid=2-s2.0-84909971050&partnerID=MN8TOARS.
    10.1021/ct500840f
  156. Sousa, S.F.; Cerqueira, N.M.F.S.A.; Brás, 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://www.scopus.com/inward/record.url?eid=2-s2.0-84906310448&partnerID=MN8TOARS.
    10.1002/qua.24689
  157. 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://www.scopus.com/inward/record.url?eid=2-s2.0-84906272546&partnerID=MN8TOARS.
    10.1021/ct500346y
  158. Calixto, A.R.; Brás, 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://www.scopus.com/inward/record.url?eid=2-s2.0-84910096204&partnerID=MN8TOARS.
    10.1021/cs500497f
  159. Araújo, 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://www.scopus.com/inward/record.url?eid=2-s2.0-84916882426&partnerID=MN8TOARS.
    10.1021/ct500570g
  160. Coimbra, J.T.S.; Moniz, T.; Brás, N.F.; Ivanova, 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://www.scopus.com/inward/record.url?eid=2-s2.0-84919389836&partnerID=MN8TOARS.
    10.1021/jp509491p
  161. 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://www.scopus.com/inward/record.url?eid=2-s2.0-84907833756&partnerID=MN8TOARS.
    10.1039/c4cp02289k
  162. Coimbra, J.T.S.; Neves, R.P.P.; Passos, Ó.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84908192323&partnerID=MN8TOARS.
    10.1016/j.cplett.2014.09.066
  163. Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "Discovery of new sites for drug binding to the hypertension-related renin-angiotensinogen complex". Chemical Biology and Drug Design 83 4 (2014): 427-439. http://www.scopus.com/inward/record.url?eid=2-s2.0-84898939513&partnerID=MN8TOARS.
    10.1111/cbdd.12258
  164. Brás, N.F.; Ribeiro, A.J.M.; Oliveira, M.; Paixão, 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): http://www.scopus.com/inward/record.url?eid=2-s2.0-84901542884&partnerID=MN8TOARS.
    10.1007/s00894-014-2271-z
  165. Ribeiro, J.V.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Chem-path-tracker: An automated tool to analyze chemical motifs in molecular structures". Chemical Biology and Drug Design 84 1 (2014): 44-53. http://www.scopus.com/inward/record.url?eid=2-s2.0-84902827564&partnerID=MN8TOARS.
    10.1111/cbdd.12349
  166. Moorthy, N.S.H.N.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84886842373&partnerID=MN8TOARS.
    10.3109/14756366.2013.779264
  167. Brás, 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://www.scopus.com/inward/record.url?eid=2-s2.0-84905505163&partnerID=MN8TOARS.
    10.1021/cs500093h
  168. Gesto, D.S.; Cerqueira, N.M.F.S.A.; 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): http://www.scopus.com/inward/record.url?eid=2-s2.0-84896563914&partnerID=MN8TOARS.
    10.1007/s00894-014-2178-8
  169. Narayana Moorthy, N.S.H.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84912036156&partnerID=MN8TOARS.
    10.1039/c4ra07961b
  170. Hari Narayana Moorthy, N.S.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84904471837&partnerID=MN8TOARS.
    10.2174/1389450115666140205152007
  171. 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 5 (2014): 1297-1310. http://www.scopus.com/inward/record.url?eid=2-s2.0-84900416783&partnerID=MN8TOARS.
    10.1107/S1399004714002570
  172. Brás, N.F.; Cerqueira, N.M.F.S.A.; Ramos, M.J.; Fernandes, P.A.. "Glycosidase inhibitors: A patent review (2008-2013)". Expert Opinion on Therapeutic Patents 24 8 (2014): 857-874. http://www.scopus.com/inward/record.url?eid=2-s2.0-84904688162&partnerID=MN8TOARS.
    10.1517/13543776.2014.916280
  173. Moorthy, N.S.H.N.; Brás, N.F.; Ramos, M.J.; Fernandes, P.A.. "Binding mode prediction and identification of new lead compounds from natural products as renin and angiotensin converting enzyme inhibitors". RSC Advances 4 38 (2014): 19550-19568. http://www.scopus.com/inward/record.url?eid=2-s2.0-84899808587&partnerID=MN8TOARS.
    10.1039/c4ra00856a
  174. Pedro Fernandes. "Prémio Nobel da Química 2013". Revista de Ciência Elementar 1 1 (2013): https://doi.org/10.24927/rce2013.002.
    10.24927/rce2013.002
  175. Moorthy, N.S.H.N.; Cerqueira, N.M.F.S.A.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84886867161&partnerID=MN8TOARS.
    10.1039/c3ra43670e
  176. 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
  177. 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
  178. Moorthy, N.S.H.N.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84876710977&partnerID=MN8TOARS.
  179. 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
  180. 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
  181. Sousa, S.F.; Ribeiro, A.J.M.; Coimbra, J.T.S.; Neves, R.P.P.; Martins, S.A.; Moorthy, N.S.H.N.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84877933286&partnerID=MN8TOARS.
    10.2174/0929867311320180002
  182. Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Parameters for molecular dynamics simulations of manganese-containing metalloproteins". Journal of Chemical Theory and Computation 9 6 (2013): 2718-2732. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879120460&partnerID=MN8TOARS.
    10.1021/ct400055v
  183. Gesto, D.S.; Cerqueira, N.M.F.S.A.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84877811918&partnerID=MN8TOARS.
    10.1021/ja310165u
  184. 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://www.scopus.com/inward/record.url?eid=2-s2.0-84877833562&partnerID=MN8TOARS.
    10.1016/j.cplett.2013.03.085
  185. 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 and Modelling 45 (2013): 13-25. http://www.scopus.com/inward/record.url?eid=2-s2.0-84884558273&partnerID=MN8TOARS.
    10.1016/j.jmgm.2013.07.007
  186. Cerqueira, N.M.F.S.A.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84885114475&partnerID=MN8TOARS.
    10.1021/ic3028034
  187. Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.; Russo, N.. "Erratum: 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 (2012) 51:49 12242-12245)". Chemical Physics Letters 579 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84880331802&partnerID=MN8TOARS.
    10.1016/j.cplett.2013.06.024
  188. Sousa, S.F.; Pinto, G.R.P.; Ribeiro, A.J.M.; Coimbra, J.T.S.; Fernandes, P.A.; Ramos, M.J.. "Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes". Journal of Computational Chemistry 34 24 (2013): 2079-2090. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885957406&partnerID=MN8TOARS.
    10.1002/jcc.23349
  189. Moorthy, N.S.H.N.; Cerqueira, N.M.F.S.A.; Ramos, M.J.; Fernandes, P.A.. "Development of ribonucleotide reductase inhibitor: A review on structure activity relationships". Mini-Reviews in Medicinal Chemistry 13 13 (2013): 1862-1872. http://www.scopus.com/inward/record.url?eid=2-s2.0-84888027525&partnerID=MN8TOARS.
    10.2174/13895575113136660090
  190. Moorthy, N.S.H.N.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "Farnesyltransferase inhibitors: A comprehensive review based on quantitative structural analysis". Current Medicinal Chemistry 20 38 (2013): 4888-4923. http://www.scopus.com/inward/record.url?eid=2-s2.0-84889569673&partnerID=MN8TOARS.
    10.2174/09298673113206660262
  191. 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
  192. 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
  193. 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
  194. 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.
  195. Silva, P.J.; Perez, M.A.S.; Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "Erratum to: Improving the study of proton transfers between amino acid side chains in solution: Choosing appropriate DFT functionals and avoiding hidden pitfalls (Theor Chem Acc, (2012) 131, 117, 10.1007/s00214-012-1179-x)". Theoretical Chemistry Accounts 132 2 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84875366125&partnerID=MN8TOARS.
    10.1007/s00214-012-1307-7
  196. 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://www.scopus.com/inward/record.url?eid=2-s2.0-84871721814&partnerID=MN8TOARS.
    10.1016/j.bbapap.2012.07.005
  197. 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
  198. 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
  199. 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
  200. Moorthy, N.S.H.N.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84864688102&partnerID=MN8TOARS.
    10.1080/1062936X.2012.666264
  201. Moorthy, N.S.H.N.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84865803335&partnerID=MN8TOARS.
    10.2174/157340612802084171
  202. 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://www.scopus.com/inward/record.url?eid=2-s2.0-84865477079&partnerID=MN8TOARS.
    10.1039/c2cp41180f
  203. De Rienzo, F.; Moura Barbosa, A.J.; 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 and Dynamics 30 3 (2012): 280-298. http://www.scopus.com/inward/record.url?eid=2-s2.0-84863873134&partnerID=MN8TOARS.
    10.1080/07391102.2012.680029
  204. 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
  205. 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
  206. Moorthy, N.S.H.N.; Brás, N.F.; Ramos, M.J.; Fernandes, P.A.. "Virtual screening and QSAR study of some pyrrolidine derivatives as a-mannosidase inhibitors for binding feature analysis". Bioorganic and Medicinal Chemistry 20 24 (2012): 6945-6959. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870054757&partnerID=MN8TOARS.
    10.1016/j.bmc.2012.10.011
  207. Brás, 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://www.scopus.com/inward/record.url?eid=2-s2.0-84865447106&partnerID=MN8TOARS.
    10.1039/c2cp41422h
  208. Ribeiro, J.V.; Cerqueira, N.M.F.S.A.; Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "CompASM: An Amber-VMD alanine scanning mutagenesis plug-in". Theoretical Chemistry Accounts 131 10 (2012): 1-7. http://www.scopus.com/inward/record.url?eid=2-s2.0-84866688979&partnerID=MN8TOARS.
    10.1007/s00214-012-1271-2
  209. Narayana Moorthy, N.S.H.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84861888793&partnerID=MN8TOARS.
    10.1007/s00044-010-9510-3
  210. 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
  211. Narayana Moorthy, N.S.H.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84859715389&partnerID=MN8TOARS.
    10.1002/ardp.201100047
  212. Silva, P.J.; Perez, M.A.S.; Brás, 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". Theoretical Chemistry Accounts 131 3 (2012): 1-6. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857467426&partnerID=MN8TOARS.
    10.1007/s00214-012-1179-x
  213. 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.
  214. Oliveira, E.F.; Cerqueira, N.M.F.S.A.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-80053318335&partnerID=MN8TOARS.
    10.1021/ja204229m
  215. Moorthy, N.S.H.N.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-84858190134&partnerID=MN8TOARS.
    10.1039/c1ra00131k
  216. Neves, A.R.; Fernandes, P.A.; Ramos, M.J.. "The accuracy of density functional theory in the description of cation-p and p-hydrogen bond interactions". Journal of Chemical Theory and Computation 7 7 (2011): 2059-2067. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960246616&partnerID=MN8TOARS.
    10.1021/ct2001667
  217. 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
  218. Hari Narayana Moorthy, N.S.; 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
  219. Brás, 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://www.scopus.com/inward/record.url?eid=2-s2.0-83455218477&partnerID=MN8TOARS.
    10.1021/ct200309v
  220. 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.
  221. Hari Narayana Moorthy, N.S.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-81355138323&partnerID=MN8TOARS.
    10.3109/14756366.2011.552885
  222. 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
  223. Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Structural analysis of a-glucosidase inhibitors by validated QSAR models using topological and hydrophobicity based descriptors". Chemometrics and Intelligent Laboratory Systems 109 2 (2011): 101-112. http://www.scopus.com/inward/record.url?eid=2-s2.0-80055094177&partnerID=MN8TOARS.
    10.1016/j.chemolab.2011.02.010
  224. Passos, O.; Fernandes, P.A.; Ramos, M.J.. "QM/MM study of the catalytic mechanism of GalNAc removal from GM2 ganglioside catalyzed by human ß-hexosaminidaseA". Journal of Physical Chemistry B 115 49 (2011): 14751-14759. http://www.scopus.com/inward/record.url?eid=2-s2.0-83455201696&partnerID=MN8TOARS.
    10.1021/jp205826n
  225. Hari Narayana Moorthy, N.S.; Ramos, M.J.; Fernandes, P.A.. "QSAR analysis of isosteviol derivatives as a-glucosidase inhibitors with element count and other descriptors". Letters in Drug Design and Discovery 8 1 (2011): 14-25. http://www.scopus.com/inward/record.url?eid=2-s2.0-78650861840&partnerID=MN8TOARS.
    10.2174/157018011793663859
  226. 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://www.scopus.com/inward/record.url?eid=2-s2.0-79954471369&partnerID=MN8TOARS.
    10.1021/ct100579w
  227. Passos, Ó.; Fernandes, P.A.; Ramos, M.J.. "Theoretical insights into the catalytic mechanism of ß-hexosaminidase". Theoretical Chemistry Accounts 129 1 (2011): 119-129. http://www.scopus.com/inward/record.url?eid=2-s2.0-79954633470&partnerID=MN8TOARS.
    10.1007/s00214-011-0904-1
  228. 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
  229. Oliveira, J.; Petrov, V.; Parola, A.J.; Pina, F.; Azevedo, J.; Teixeira, N.; Brás, 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://www.scopus.com/inward/record.url?eid=2-s2.0-79951538171&partnerID=MN8TOARS.
    10.1021/jp110593c
  230. Brás, 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://www.scopus.com/inward/record.url?eid=2-s2.0-79953239442&partnerID=MN8TOARS.
    10.1002/qua.22631
  231. 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://www.scopus.com/inward/record.url?eid=2-s2.0-79957584233&partnerID=MN8TOARS.
    10.1021/jp200075s
  232. Cerqueira, N.M.F.S.A.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-79952168691&partnerID=MN8TOARS.
    10.1002/qua.22738
  233. Cerqueira, N.M.F.S.A.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-79955900191&partnerID=MN8TOARS.
    10.1021/ct1002219
  234. 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://www.scopus.com/inward/record.url?eid=2-s2.0-77955561344&partnerID=MN8TOARS.
    10.1021/ct900649e
  235. 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
  236. Sousa, S.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Virtual screening in drug design and development". Combinatorial Chemistry and High Throughput Screening 13 5 (2010): 442-453. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955767207&partnerID=MN8TOARS.
    10.2174/138620710791293001
  237. Brás, N.F.; Gonçalves, 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-77953906402&partnerID=MN8TOARS.
    10.1021/bi100410q
  238. Dourado, D.F.A.R.; 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-77957825421&partnerID=MN8TOARS.
    10.1021/jp1053875
  239. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-77956594850&partnerID=MN8TOARS.
    10.1021/ct1002175
  240. Brás, N.F.; Gonçalves, R.; Mateus, N.; Fernandes, P.A.; Ramos, M.J.; De Freitas, V.. "Inhibition of pancreatic elastase by polyphenolic compounds". Journal of Agricultural and Food Chemistry 58 19 (2010): 10668-10676. http://www.scopus.com/inward/record.url?eid=2-s2.0-78049265413&partnerID=MN8TOARS.
    10.1021/jf1017934
  241. 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
  242. 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
  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. http://www.scopus.com/inward/record.url?eid=2-s2.0-77249136920&partnerID=MN8TOARS.
    10.1021/jp910958u
  244. 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
  245. 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
  246. Bráa, N.F.; Fernandes, P.A.; Ramos, M.J.. "QM/MM studies on the ß-galactosidase catalytic mechanism: Hydrolysis and transglycosylation reactions". Journal of Chemical Theory and Computation 6 2 (2010): 421-433. http://www.scopus.com/inward/record.url?eid=2-s2.0-77950130195&partnerID=MN8TOARS.
    10.1021/ct900530f
  247. Moura-Tamames, S.A.; Ramos, M.J.; Fernandes, P.A.. "Modelling ß-1,3-exoglucanase-saccharide interactions: Structure of the enzyme-substrate complex and enzyme binding to the cell wall". Journal of Molecular Graphics and Modelling 27 8 (2009): 908-920. http://www.scopus.com/inward/record.url?eid=2-s2.0-67349243347&partnerID=MN8TOARS.
    10.1016/j.jmgm.2009.01.007
  248. Dourado, D.F.A.R.; Fernandes, P.A.; Ramos, M.J.. "Glutathione transferase A1-1: Catalytic role of water". Theoretical Chemistry Accounts 124 1-2 (2009): 71-83. http://www.scopus.com/inward/record.url?eid=2-s2.0-70449529533&partnerID=MN8TOARS.
    10.1007/s00214-009-0582-4
  249. 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
  250. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme". Bioorganic and Medicinal Chemistry 17 9 (2009): 3369-3378. http://www.scopus.com/inward/record.url?eid=2-s2.0-65249179022&partnerID=MN8TOARS.
    10.1016/j.bmc.2009.03.055
  251. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349310441&partnerID=MN8TOARS.
    10.1039/b904404c
  252. 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.
  253. 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.
  254. 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.
  255. Sousa, S.F.; Carvalho, E.S.; Ferreira, D.M.; Tavares, I.S.; Fernandes, P.A.; Ramos, M.J.; Gomes, J.A.N.F.. "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://www.scopus.com/inward/record.url?eid=2-s2.0-70349932424&partnerID=MN8TOARS.
    10.1002/jcc.21304
  256. 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
  257. Brás, 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-64149094355&partnerID=MN8TOARS.
    10.1007/s00214-009-0507-2
  258. 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://www.scopus.com/inward/record.url?eid=2-s2.0-64549135410&partnerID=MN8TOARS.
    10.1002/jcc.21086
  259. Cerqueira, N.M.F.S.A.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-58949084789&partnerID=MN8TOARS.
    10.1002/prot.22146
  260. 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
  261. Ramos, M.J.; Fernandes, P.A.. "Computational enzymatic catalysis". Accounts of Chemical Research 41 6 (2008): 689-698. http://www.scopus.com/inward/record.url?eid=2-s2.0-47249103804&partnerID=MN8TOARS.
    10.1021/ar7001045
  262. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-47349089381&partnerID=MN8TOARS.
    10.2174/092986708784638825
  263. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-48949117560&partnerID=MN8TOARS.
    10.2174/092986708784221467
  264. Viegas, A.; Brás, N.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Prates, J.A.M.; Fontes, C.M.G.A.; 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-42649116746&partnerID=MN8TOARS.
    10.1111/j.1742-4658.2008.06401.x
  265. Dourado, D.F.A.R.; Fernandes, P.A.; Ramos, M.J.. "Mammalian cytosolic glutathione transferases". Current Protein and Peptide Science 9 4 (2008): 325-337. http://www.scopus.com/inward/record.url?eid=2-s2.0-49249135353&partnerID=MN8TOARS.
    10.2174/138920308785132677
  266. Brás, N.F.; Cerqueira, N.M.F.S.A.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-47549090465&partnerID=MN8TOARS.
    10.1002/qua.21755
  267. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-45449099914&partnerID=MN8TOARS.
    10.1007/s00214-008-0432-9
  268. 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
  269. Dourado, D.F.A.R.; Fernandes, P.A.; Mannervik, B.; Ramos, M.J.. "Glutathione transferase: New model for glutathione activation". Chemistry - A European Journal 14 31 (2008): 9591-9598. http://www.scopus.com/inward/record.url?eid=2-s2.0-55049084123&partnerID=MN8TOARS.
    10.1002/chem.200800946
  270. Marques, A.T.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics simulations of the amyloid-beta binding alcohol dehydrogenase (ABAD) enzyme". Bioorganic and Medicinal Chemistry 16 21 (2008): 9511-9518. http://www.scopus.com/inward/record.url?eid=2-s2.0-53849140775&partnerID=MN8TOARS.
    10.1016/j.bmc.2008.09.043
  271. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-47549102060&partnerID=MN8TOARS.
    10.1002/qua.21713
  272. Marques, A.T.; Antunes, A.; Fernandes, P.A.; Ramos, M.J.. "Computational optimization of AG18051 inhibitor for amyloid-ß binding alcohol dehydrogenase enzyme". International Journal of Quantum Chemistry 108 11 (2008): 1982-1991. http://www.scopus.com/inward/record.url?eid=2-s2.0-47549087365&partnerID=MN8TOARS.
    10.1002/qua.21716
  273. Brás, 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-55349124348&partnerID=MN8TOARS.
    10.1002/jcc.21013
  274. Carvalho, A.T.P.; Swart, M.; Van Straten, 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://www.scopus.com/inward/record.url?eid=2-s2.0-40549093328&partnerID=MN8TOARS.
    10.1021/jp7104665
  275. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33847650393&partnerID=MN8TOARS.
    10.1002/jcc.20566
  276. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33846840870&partnerID=MN8TOARS.
    10.1021/ja067103n
  277. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845995126&partnerID=MN8TOARS.
    10.1002/qua.21193
  278. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845967151&partnerID=MN8TOARS.
    10.1002/qua.21192
  279. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-34247548408&partnerID=MN8TOARS.
    10.1002/jcc.20577
  280. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-36148995097&partnerID=MN8TOARS.
    10.1021/ct6003824
  281. Sousa Moreira, I.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-33947123052&partnerID=MN8TOARS.
    10.2174/187152007780058687
  282. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-34047271259&partnerID=MN8TOARS.
    10.1021/jp067096p
  283. 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 and Modelling 26 3 (2007): 634-642. http://www.scopus.com/inward/record.url?eid=2-s2.0-34848852204&partnerID=MN8TOARS.
    10.1016/j.jmgm.2007.03.009
  284. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-35948998054&partnerID=MN8TOARS.
    10.1021/jp0746594
  285. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548202669&partnerID=MN8TOARS.
    10.1021/jp072538y
  286. 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 Genetics 68 4 (2007): 803-812. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548779127&partnerID=MN8TOARS.
    10.1002/prot.21396
  287. 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 Genetics 69 3 (2007): 466-475. http://www.scopus.com/inward/record.url?eid=2-s2.0-35448995715&partnerID=MN8TOARS.
    10.1002/prot.21536
  288. Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Understanding ribonucleotide reductase inactivation by gemcitabine". Chemistry - A European Journal 13 30 (2007): 8507-8515. http://www.scopus.com/inward/record.url?eid=2-s2.0-35348969874&partnerID=MN8TOARS.
    10.1002/chem.200700260
  289. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "General performance of density functionals". Journal of Physical Chemistry A 111 42 (2007): 10439-10452. http://www.scopus.com/inward/record.url?eid=2-s2.0-35748980308&partnerID=MN8TOARS.
    10.1021/jp0734474
  290. Cerqueira, N.M.F.S.A.; 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://www.scopus.com/inward/record.url?eid=2-s2.0-34248170858&partnerID=MN8TOARS.
    10.2174/157489207779561408
  291. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33751235864&partnerID=MN8TOARS.
    10.1007/s00214-006-0170-9
  292. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33751248238&partnerID=MN8TOARS.
    10.1007/s00214-006-0151-z
  293. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Theoretical studies on farnesyltransferase: The distances paradox explained". Proteins: Structure, Function and Genetics 66 1 (2007): 205-218. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845671721&partnerID=MN8TOARS.
    10.1002/prot.21219
  294. Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Detailed microscopic study of the full ZipA:FtsZ interface". Proteins: Structure, Function and Genetics 63 4 (2006): 811-821. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646784622&partnerID=MN8TOARS.
    10.1002/prot.20944
  295. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33745467541&partnerID=MN8TOARS.
    10.1021/jp054760d
  296. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646590228&partnerID=MN8TOARS.
    10.2174/138955706776876276
  297. Carvalho, A.T.P.; Fernandes, P.A.; Ramos, M.J.. "Determination of the ¿pKa between the active site cysteines of thioredoxin and DsbA". Journal of Computational Chemistry 27 8 (2006): 966-975. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646560034&partnerID=MN8TOARS.
    10.1002/jcc.20404
  298. Marques, A.T.; Antunes, A.; Fernandes, P.A.; Ramos, M.J.. "Comparative evolutionary genomics of the HADH2 gene encoding Aß-binding alcohol dehydrogenase/17ß-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10)". BMC Genomics 7 (2006): http://www.scopus.com/inward/record.url?eid=2-s2.0-33748344899&partnerID=MN8TOARS.
    10.1186/1471-2164-7-202
  299. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748541278&partnerID=MN8TOARS.
    10.1021/jp056855l
  300. Carvalho, A.P.; Fernandes, P.A.; Ramos, M.J.. "Similarities and differences in the thioredoxin superfamily". Progress in Biophysics and Molecular Biology 91 3 (2006): 229-248. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645115156&partnerID=MN8TOARS.
    10.1016/j.pbiomolbio.2005.06.012
  301. Fernandes, P.A.; Araújo, M.L.A.C.; Barbosa, A.J.M.; Alves, C.N.; Ferreira, Z.Q.; Gonzalez, C.R.-N.; Lima, C.F.R.A.C.; et al. "Lead optimisation: Improving the affinity of the antiretrovirals nelfinavir and amprenavir for HIV-1 protease". Letters in Drug Design and Discovery 3 6 (2006): 383-389. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746712231&partnerID=MN8TOARS.
    10.2174/157018006777805576
  302. Cerqueira, N.M.F.S.A.; 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33751297639&partnerID=MN8TOARS.
    10.1021/jp0608269
  303. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845958917&partnerID=MN8TOARS.
    10.1021/jm060698c
  304. 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
  305. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Protein-ligand docking: Current status and future challenges". Proteins: Structure, Function and Genetics 65 1 (2006): 15-26. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748276474&partnerID=MN8TOARS.
    10.1002/prot.21082
  306. Pereira, S.; Cerqueira, N.M.F.S.A.; 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 35 2 (2006): 125-135. http://www.scopus.com/inward/record.url?eid=2-s2.0-29944434730&partnerID=MN8TOARS.
    10.1007/s00249-005-0026-6
  307. Ramos, M.J.; Fernandes, P.A.. "Atomic-level rational drug design". Current Computer-Aided Drug Design 2 1 (2006): 57-81. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746206391&partnerID=MN8TOARS.
    10.2174/157340906776056464
  308. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645676926&partnerID=MN8TOARS.
    10.1021/jp053275f
  309. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-32444433270&partnerID=MN8TOARS.
    10.1007/s00214-005-0672-x
  310. Cerqueira, N.M.F.S.A.; 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645979395&partnerID=MN8TOARS.
    10.1529/biophysj.104.054627
  311. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-12944324735&partnerID=MN8TOARS.
    10.1007/s00775-004-0612-6
  312. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-17144411095&partnerID=MN8TOARS.
    10.1021/ja046662w
  313. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-11244321501&partnerID=MN8TOARS.
    10.1529/biophysj.104.048207
  314. Ramos, M.J.; Fernandes, P.A.. "Computer modeling and research in the classroom". Journal of Chemical Education 82 7 (2005): 1021-1025. http://www.scopus.com/inward/record.url?eid=2-s2.0-21244459676&partnerID=MN8TOARS.
  315. 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 SPEC. (2005): 11-18. http://www.scopus.com/inward/record.url?eid=2-s2.0-24344502228&partnerID=MN8TOARS.
    10.1016/j.theochem.2004.12.049
  316. Fernandes, P.A.; Henriques, E.S.; Pande, V.; Ramos, M.J.; Maia, A.R.R.; Almeida, A.A.S.; Silva, B.F.B.; et al. "New designs for inhibitors of the NF-¿B: DNA binding". Theoretical Chemistry Accounts 113 4 (2005): 197-204. http://www.scopus.com/inward/record.url?eid=2-s2.0-21044448195&partnerID=MN8TOARS.
    10.1007/s00214-005-0628-1
  317. Cerqueira, N.M.F.S.A.; 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-19044394312&partnerID=MN8TOARS.
    10.2174/0929867054020981
  318. 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 SPEC. (2005): 125-129. http://www.scopus.com/inward/record.url?eid=2-s2.0-24344434552&partnerID=MN8TOARS.
    10.1016/j.theochem.2005.03.022
  319. 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 SPEC. (2005): 141-146. http://www.scopus.com/inward/record.url?eid=2-s2.0-24344466892&partnerID=MN8TOARS.
    10.1016/j.theochem.2004.12.046
  320. Ramos, M.J.; Magalhães, A.L.; Melo, A.S.; Fernandes, P.A.. "Foreword". Journal of Molecular Structure: THEOCHEM 729 1-2 SPEC. (2005): http://www.scopus.com/inward/record.url?eid=2-s2.0-24344432007&partnerID=MN8TOARS.
    10.1016/j.theochem.2005.04.028
  321. Ramos, M. J.; Fernandes, P. A.; Melo, A.; Ramos, M.J.; Fernandes, P.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
  322. Cerqueira, N.M.F.S.A.; 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-9244264943&partnerID=MN8TOARS.
    10.1002/jcc.20127
  323. Fernandes, P.A.; Ramos, M.J.. "Theoretical Insights into the Mechanism for Thiol/Disulfide Exchange". Chemistry - A European Journal 10 1 (2004): 257-266. http://www.scopus.com/inward/record.url?eid=2-s2.0-0347719283&partnerID=MN8TOARS.
    10.1002/chem.200305343
  324. 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-¿B: DNA binding inhibitory properties". Journal of Molecular Structure: THEOCHEM 685 1-3 (2004): 73-82. http://www.scopus.com/inward/record.url?eid=2-s2.0-6944250787&partnerID=MN8TOARS.
    10.1016/j.theochem.2004.06.027
  325. Cerqueira, N.M.F.S.A.; Fernandes, 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 SPEC. (2004): 53-65. http://www.scopus.com/inward/record.url?eid=2-s2.0-11144306568&partnerID=MN8TOARS.
    10.1016/j.theochem.2003.10.073
  326. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-0345763175&partnerID=MN8TOARS.
    10.1002/jcc.10375
  327. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-3042547835&partnerID=MN8TOARS.
    10.1002/jcc.20054
  328. 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. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000183592000013&KeyUID=WOS:000183592000013.
    10.1021/jp0223096
  329. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-0344271775&partnerID=MN8TOARS.
    10.1023/A:1027347527385
  330. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037950581&partnerID=MN8TOARS.
    10.1021/ja0208613
  331. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-0347592865&partnerID=MN8TOARS.
    10.1007/s00214-003-0476-9
  332. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-0347228946&partnerID=MN8TOARS.
    10.1002/chem.200304948
  333. 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036976685&partnerID=MN8TOARS.
    10.1007/s00214-002-0393-3
  334. Fernandes, P. A.; Cordeiro, Mnds; Gomes, Janf. "Molecular simulation of the interface between two immiscible electrolyte solutions". Journal of Physical Chemistry B 105 5 (2001): 981-993. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000166846100011&KeyUID=WOS:000166846100011.
    10.1021/jp002571j
  335. Gomes, Janf; Fernandes, P. A.; Natalia, M.; Cordeiro, D. S.. "Simulation of liquid/liquid interfaces and ion transfer". Abstracts of Papers of the American Chemical Society 220 (2000): U232-U232. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000166091201182&KeyUID=WOS:000166091201182.
  336. Fernandes, P.A.; Natália, M.; Cordeiro, D.S.; Gomes, J.A.N.F.. "Influence of Ion Size and Charge in Ion Transfer Processes Across a Liquid|Liquid Interface". Journal of Physical Chemistry B 104 10 (2000): 2278-2286. http://www.scopus.com/inward/record.url?eid=2-s2.0-0001606789&partnerID=MN8TOARS.
  337. Fernandes, P.A.; Cordeiro, M.N.D.S.; Gomes, J.A.N.F.. "Molecular dynamics simulation of the water/2-heptanone liquid-liquid interface". Journal of Physical Chemistry B 103 30 (1999): 6290-6299. http://www.scopus.com/inward/record.url?eid=2-s2.0-0000578941&partnerID=MN8TOARS.
  338. Fernandes, P.A.; Cordeiro, M.N.D.S.; Gomes, J.A.N.F.. "Molecular dynamics simulation of liquid 2-heptanone, pure and saturated with water". Journal of Physical Chemistry B 103 7 (1999): 1176-1184. http://www.scopus.com/inward/record.url?eid=2-s2.0-0344004660&partnerID=MN8TOARS.
  339. Fernandes, P.A.; Cordeiro, M.N.D.S.; Gomes, J.A.N.F.; Fernandes, P. A.; Cordeiro, Mnds; Gomes, Janf. "Molecular dynamics simulation of the water/1,2-dichloroethane interface". Journal of Molecular Structure: THEOCHEM 463 1-2 (1999): 151-156. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033597061&partnerID=MN8TOARS.
    10.1016/S0166-1280(98)00405-9
  340. Fernandes, P.A.; Cordeiro, M.N.D.S.; Gomes, J.A.N.F.. "Molecular Dynamics Study of the Transfer of Iodide across Two Liquid/Liquid Interfaces". Journal of Physical Chemistry B 103 42 (1999): 8930-8939. http://www.scopus.com/inward/record.url?eid=2-s2.0-0000480945&partnerID=MN8TOARS.
    10.1021/jp9916945
  341. Fernandes, P.A.; Carvalho, A.P.; Ramalho, J.P.P.. "Path integral Monte Carlo simulations: Study of the efficiency of energy estimators". The Journal of Chemical Physics 103 13 (1995): 5720-5724. http://www.scopus.com/inward/record.url?eid=2-s2.0-0000945185&partnerID=MN8TOARS.
Capítulo de livro
  1. Teixeira, C.S.S.; Fernandes, H.S.; Fernandes, P.A.; Ramos, M.J.; Cerqueira, N.M.F.S.A.. "Cancer therapies based on enzymatic amino acid depletion". 623-651. 2017.
  2. Sousa, Sergio F.; Coimbra, Joao T. S.; Fernandes, Pedro A.; Marino, Tiziana; Ramos, Maria J.; Russo, Nino. "Molecular Dynamics Analysis of FAAH Complexed with Anandamide". editado por Nascimento, M. A. C.; Maruani, J.; Brandas, E. J.; DelgadoBarrio, G., 114-130. 2015.
    10.1007/978-3-319-14397-2_7
  3. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes". 299-330. 2010.
    10.1007/978-90-481-3034-4_11
  4. Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Computational Determination of the Relative Free Energy of Binding – Application to Alanine Scanning Mutagenesis". 305-339. 2007.
    10.1007/1-4020-5372-X_6
Livro
  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

Outros

Outra produção
  1. Alkyl vs Aryl Modifications: A Comparative Study on Modular Modifications of Triphenylphosphonium Mitochondrial Vectors. 2021. How Chee Ong; João T.S. Coimbra; Maria Joa~o Ramos; Bengang Xing; Pedro Alexandrino Fernandes; Felipe Garcia. https://doi.org/10.26434/chemrxiv.14445327.v1.
    10.26434/chemrxiv.14445327.v1
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2020/04/01 PLENARY/INVITED TALKS: I have given ~80 plenary and invited conferences in the last 20 years. The detailed list can be found at the webpage: www.fc.up.pt/pessoas/pafernan/talks.html Many different conferences and seminars.

Orientação

Título / Tema
Papel desempenhado 		Curso (Tipo)
Instituição / Organização
1999 - 2020 ACADEMIC SUPERVISION: During the last 20 years I have supervised and co-supevised a total of 35 PhD and Post-Doc degrees. I haven't kept track of my supervision activities during the MSc degrees. The full list of students I have supervised and the respective degrees can be found at the webpage: www.fc.up.pt/pessoas/pafernan/supervision.html
Orientador

Júri de grau académico

Tema
Tipo de participação 		Nome do candidato (Tipo de grau)
Instituição / Organização
2020 ACADEMIC JURIES: I have participated in 120 MSc and PhD juries in the last 20 years. The complete list and details can be found at the webpage: www.fc.up.pt/pessoas/pafernan/juries.html The full list of candidates can be found at the webpage www.fc.up.pt/pessoas/pafernan/juries.html (Outro)

Arbitragem científica em conferência

Nome da conferência Local da conferência
2000 - 2020 CHAIRPERSON: Even though I never kept a record of my role as a chairman, I have acted as a chairman in most of the conferences in which I present plenary/invited talks.

Arbitragem científica em revista

Nome da revista (ISSN) Editora
2000 - 2020 PEER-REVIEWING ACTIVITY: I have reviewed over 200 papers to at least 42 international journals in the last 20 years. The list of the journals to which I have contributed with peer-reviews are listed in the webpage: www.fc.up.pt/pessoas/pafernan/revisions.html

Comissão de avaliação

Descrição da atividade
Tipo de assessoria 		Instituição / Organização Entidade financiadora
2007 - 2020 EVALUATION OF RESEARCH PROJECTS: I have acted as evaluator of many financing agencies, such as: Fondecyt (Chile); H2020 (EU); National Science Center (Poland); Dutch Research Council (The Netherlands) Flanders Research Council (Flanders, The Netherlands) Czech Science Foundation (Czech Republic) Swiss National Science Foundation (Switzerland) Foundation for Science and Technology (Portugal) Natural Sciences and Engineering Research Council of Canada (Canada)
Avaliador
 Comisión Nacional de Investigación Científica y Tecnológica Fondo Nacional de Desarrollo Científico y Tecnológico

H2020 - FET-OPEN-European Union

European Research Council

National Science Center of Poland

Nederlandse Organisatie voor Wetenschappelijk Onderzoek

Flanders Research Council

Grantová agentura Ceské republiky

Schweizerischer Nationalfonds zur Förderung der wissenschaftlichen Forschung

Fundação para a Ciência e a Tecnologia

Natural Sciences and Engineering Research Council of Canada

Consultoria / Parecer

Descrição da atividade Instituição / Organização
2014 - 2019 CONSULTANCY: I have provided consultancy in the field of biotechnology and drug discovery for several national/multinational companies, such as Pepsico NY (Biotechnology), Bial (Pharmaceutic Company) and CFER Labs (Biotechnology).

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
1999 - 2020 TEACHING: I am a staff professor at the University of Porto, where I taught an average of 9-10 hours/week during the last 21 years. I taught more than 20 different courses to many different academic degrees, such as the BSc in Chemistry, Bsc in Biochemistry, MSc in Chemistry, MSc in Biochemistry, MSc in Bioinformatics and Computational Biology, MSc in Synthetic Biology, PhD in Chemistry, and PhD in Sustainable Chemistry. My courses focus on Quantum Chemistry/Computational Chemistry/Drug Discovery/Molecular Modelling.

Membro de comissão

Descrição da atividade
Tipo de participação 		Instituição / Organização
2012 - 2020 MEMBERSHIP IN DIRECTING BODIES: Portuguese Delegate in the Division of Computational Chemistry of the EuCHeMS. Delegate at the IUPAC Taskforce for the Definition of terms in Physical Organic Chemistry. Member of the Senate of the University of Porto. Member of the Directive Commission of the Master in Biochemistry of the University of Porto. Member of the Directive Commission of the Master of Bioinformatics of the University of Porto. Member of the Directive Commission of the Doctorate in Chemistry of the University of Porto.
Distinções

Prémio

2010 Best talk in the International Congress "11th Eurasia Conference on Chemical Sciences", Jordan, 2010

Título

2022 Associate Editor of the journal Molecules
MDPI AG, Suiça
2010 Habilitation in Chemistry
Universidade do Porto, Portugal

Outra distinção

2020 Eleven Journal Covers, such as "Studies on neuraminidase inhibition", "General Performance of Density Functionals", Virtual Screening of Compound Libraries", "Overview of ribonucleotide reductase inhibitors"
2018 Associate Editor of the Journal "Theoretical Chemistry Accounts" (Springer)
2015 Editor of the journal "Frontiers in Chemistry"
2007 Article "General performance of density functionals" frequently classified as Highly Cited in the ISI Web of Knowledge
2007 Article "Hot spots-A review of the protein-protein interface determinant amino-acid residues" frequently classified as Highly Cited by the ISI Web of Knowledge.
2006 Article "Protein-ligand docking: Current status and future challenges" frequently classified as Highly Cited in the ISI Web of Knowledge
2005 Nomination as Portuguese Delegate at the Young Chemists Workshop On Bio-Physical Chemistry meets Molecular Medicine, Sesimbra, Portugal
2003 Nomination as Portuguese Delegate at the CERC3 Young Chemists Workshop on Computer Modelling Of Chemical And Biological Systems, Porto, Portugal