Pedro Manuel Azevedo Alexandrino Fernandes (CF15-D864-2EE8)

Curriculum Vitae

Pedro Manuel Azevedo Alexandrino Fernandes

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

Telephone

220402667 Ext.: 30667 (Professional)

Moradas

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

Websites

http://www.fc.up.pt/pessoas/pafernan (Professional)

Domínios de atuação

Exact Sciences - Chemical Sciences

Idiomas

Idioma	Conversação	Leitura	Escrita	Compreensão	Peer-review
Portuguese (Idioma materno)
French	Upper intermediate (B2)	Proficiency (C2)	Upper intermediate (B2)	Proficiency (C2)	Proficiency (C2)
English	Advanced (C1)	Proficiency (C2)	Advanced (C1)	Proficiency (C2)	Proficiency (C2)

Formação

	Grau	Classificação
2010/01/06 - 2010/01/07 Concluded	Química (Título de Agregado) Universidade do Porto Faculdade de Ciências, Portugal	Unanimidade
2000/02/29 Concluded	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 Concluded	Química (Licenciatura) Universidade do Porto Faculdade de Ciências, Portugal	15

Percurso profissional

Teaching in Higher Education

	Categoria Profissional Instituição de acolhimento	Empregador
2024/03/14 - Atual	Full Professor (University Teacher)	Universidade do Porto Faculdade de Ciências, Portugal
	Universidade do Porto Faculdade de Ciências, Portugal
2009/03/01 - 2024/03/14	Associate Professor (University Teacher)	Universidade do Porto, Portugal

1999/12/01 - 2009/03/01	Invited Assistant Professor (University Teacher)	Universidade do Porto Faculdade de Ciências, Portugal

Projetos

Grant

	Designação	Financiadores
2025/02/15 - 2028/02/14	Biodiversity2Drugs BiodivNBS/0009/2023 Principal investigator REQUIMTE LAQV Porto, Portugal	Fundação para a Ciência e a Tecnologia Ongoing

Contract

	Designação	Financiadores
2012/05/01 - Atual	New drugs for hypertension info:eu-repo/grantAgreement/FCT/COMPETE/121744/PT Researcher REQUIMTE LAQV Porto, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2023/01/01 - 2028/12/31	Enzymatic Deconstruction of Thermoset Plastics En’Zync – 0072891 EnZync 0072891 Co-Principal Investigator (Co-PI) REQUIMTE LAQV Porto, Portugal	Danmarks Tekniske Universitet The Novo Nordisk Foundation Center for Biosustainability Ongoing
2023/02/01 - 2026/01/31	Multi-target Teragnostics for the Alzheimer Disease 2022.06064.PTDC Researcher REQUIMTE LAQV Porto, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2021/01/01 - 2025/12/31	Associated Laboratory for Green Chemistry - Clean Technologies and Processes LA/P/0008/2020 10.54499/LA/P/0008/2020 UID/QUI/50006/2019 Universidade do Porto Faculdade de Ciências, Portugal Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal Universidade Nova de Lisboa, Portugal Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal Universidade de Aveiro, Portugal Universidade de Évora, Portugal Unidade de Investigação Vidro e Cerâmica para as Artes, Portugal Universidade de Lisboa Instituto Dom Luiz, Portugal Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2021/03/29 - 2024/03/28	Murderous Venom - Towards a Universal Antidote Against Snakebite PTDC/QUI-OUT/1401/2020 Principal investigator 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 Principal investigator REQUIMTE LAQV Porto, Portugal	EuroHPC Joint Undertaking
2023/03/08 - 2024/03/07	Murderous Venom- An Universal and Affordable Antidote Against Snakebite EHPC-REG-2022R03-205 Universidade do Porto Faculdade de Ciências, Portugal REQUIMTE LAQV Porto, Portugal	Partnership for Advanced Computing In Europe Concluded
2022/06/01 - 2023/05/31	The mechanism of action of the sPLA2-like toxin of viper venom. 2021.09753.CPCA Principal investigator REQUIMTE LAQV Porto, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2020 - 2023	2019215204-Biodegrading Plastics. 2019215204 Researcher REQUIMTE LAQV Porto, Portugal Universidade do Porto Departamento de Química e Bioquímica, Portugal	PRACE – Partnership for Advanced Computing in Europe Ongoing
2022/06/01 - 2022/08/31	An Universal and Affordable Antidote for Snakebite EHPC-BEN-2022B05-080 Principal investigator REQUIMTE LAQV Porto, Portugal	EuroHPC Joint Undertaking Concluded
2020 - 2020	Drug discovery targeting Covid-19 XSEDE ASC200029 COVID-19-49 Researcher Universidade do Porto Departamento de Química e Bioquímica, Portugal REQUIMTE LAQV Porto, Portugal	Extreme Science and Engineering Discovery Environment- National Science Foundation Partnership for Advanced Computing In Europe Concluded
2019 - 2020	Enzyme instantaneous disorder as a key player in the catalytic power of enzymes CHM151-2019 Principal investigator Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Oak Ridge National Laboratory Ongoing
2018 - 2020	New Biocatalysts for Green Crude Oil Desulfurization PTDC/QUI-QFI/28714/2017 Principal investigator Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018 - 2020	Interdisciplinary in silico, organic synthesis, in vitro, and in vivo studies towards new anti-diabetic flavonoid scaffolds PTDC/MED-QUI/29241/2017 Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2015 - 2020	TCCM - Theoretical Chemistry and Computational Modelling ITN-EJD-642294 Researcher Universidade do Porto Faculdade de Ciências, Portugal	Concluded
2016 - 2019	(Fe)rrying plants to prevent chlorosis PTDC/AGR-PRO/3515/2014 Researcher REQUIMTE LAQV Porto, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2016 - 2019	New Technologies for three Health Challenges of Modern Societies: Diabetes, Drug Abuse and Kidney Diseases NORTE-01-0145-FEDER-000024 Principal investigator REQUIMTE LAQV Porto, Portugal	Comissao de Coordenacao e Desenvolvimento Regional do Norte Concluded
2018 - 2018	Bacterial initiation factors and termination factors as new targets for novel antibiotics PRACE 2018184467 Researcher REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal Universidade do Porto Departamento de Química e Bioquímica, Portugal	Partnership for Advanced Computing In Europe Concluded
2013/01/01 - 2018	ENZYMATIC CATALYSIS - seeking a global picture info:eu-repo/grantAgreement/FCT/COMPETE/128544/PT Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2014 - 2015	Consensus Scoring – A new methodology to identify lead compounds for the pharmaceutical industry EXPL/QEQ-COM/1125/2013 Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2011/01/01 - 2012/12/31	Strategic Project - LA 6 - 2011-2012 PEst-C/EQB/LA0006/2011 Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2009/01/02 - 2012/06/30	Novas Arquitecturas Moleculares para Combater Processos Infecciosos PTDC/QUI/67915/2006 Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2010 - 2012	Molecular Mechanisms of Hypercholesterolemia: New insights and New Therapeutic Strategies info:eu-repo/grantAgreement/FCT/5876-PPCDTI/102760/PT Principal investigator Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Universidade do Algarve Faculdade de Ciências e Tecnologia Concluded
2010 - 2012	New Biomolecular Force Field EXPL/QEQ-COM/1125/2013	Fundação para a Ciência e a Tecnologia
2008/01/01 - 2011/06/30	Phenogenetic drift in evolution: insights into the genetic basis of vertebrate developmental genes PTDC/BIA-BDE/69144/2006 Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2009/01/02 - 2011	Novel Key Molecular Architectures to Target Infection info:eu-repo/grantAgreement/FCT/5876-PPCDTI/67915/PT Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2008 - 2010	Evolution of Phenogenetic Changes: Genetic Study of the Variation of Development Genes in Vertebrates 19. PTDC/BIA-BDE/69144/2006 Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2008 - 2010	The modulation of retinoic acid signalling pathways by environmental pollutants in teleosts info:eu-repo/grantAgreement/FCT/5876-PPCDTI/68106/PT Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Universidade do Algarve Faculdade de Ciências e Tecnologia Concluded
2008 - 2010	Spectroscopic and Computational Studies on the Catalytic Mechanism of Nitrate Reductase. PTDC/QUI/67052/2006 Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Concluded
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 Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2008 - 2010	Drug design towards the HIV-1 virus. info:eu-repo/grantAgreement/FCT/5876-PPCDTI/68302/PT Principal investigator Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Universidade do Algarve Faculdade de Ciências e Tecnologia Concluded
2005 - 2008	Enzymatic catalysis: mechanistic studies of cancer-related human enzymes info:eu-repo/grantAgreement/FCT/POCI/61563/PT Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Universidade do Algarve Faculdade de Ciências e Tecnologia Concluded
2004 - 2007	HPC Infrastructure for Computational Chemistry at the Associated Laboratory REQUIMTE CONC-REEQ/1236/2001 CONC-REEQ/1236/2001 Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2004 - 2005	Molecular Determinants of Ligand Specificity in the Family 11 Carbohydrate Binding Modules ReqMol Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Concluded
2000 - 2003	Inhibition Mechanisms of Radical Enzymes - A QM/MM Study POCTI/35376/QUI/1999 Researcher Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Other

	Designação	Financiadores
2019/01/01 - 2019/12/31	Laboratório Associado para a Química Verde - Tecnologias e Processos Limpos UID/QUI/50006/2019 LA/P/0008/2020 10.54499/LA/P/0008/2020 Universidade do Porto Faculdade de Ciências, Portugal Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal Universidade Nova de Lisboa, Portugal Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal Universidade de Aveiro, Portugal Universidade de Évora, Portugal Unidade de Investigação Vidro e Cerâmica para as Artes, Portugal Universidade de Lisboa Instituto Dom Luiz, Portugal Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Produções

Publications

Book	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
Book chapter	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. 10.1016/b978-0-323-46144-3.00024-6 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 Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ. "Ribonucleotide Reductase – Computational Studies". 2013. 10.1007/978-3-642-16712-6_264 Brás, NF; Coimbra, JTS; Neves, RPP; Cerqueira, NMFSA; Sousa, SF; Fernandes, PA; Ramos, MJ. "Computational Biochemistry". 2013. 10.1016/b978-0-12-409547-2.10833-9 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 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
Conference abstract	Fernandes, PA. "THE MOLECULAR MECHANISM OF ACTION OF SNAKE VENOM TOXINS - A COMPUTATIONAL PERSPECTIVE". 2024. Luís M. C. Teixeira; Coimbra, João TS; Ramos, Maria João; Fernandes, Pedro Alexandrino. Corresponding author: Fernandes, Pedro Alexandrino. "Blocking SARS-CoV-2 Infection: Inhibiting the Human Enzyme TMPRSS2". Trabalho apresentado em 15th University of Porto Young Research Meeting (IJUP), Porto, 2022. Published Luís M. C. Teixeira; Coimbra, João TS; Ramos, Maria João; Fernandes, Pedro Alexandrino. "The Reaction Mechanism of SARS-CoV-2 Spike Protein Cleavage by TMPRSS2: A Quantum Mechanics/Molecular Mechanics Study". Trabalho apresentado em XXVI Galician-Portugues International Conference on Chemistry, Santiago de Compostela, 2022. Published Sousa, CF; Coimbra, JT; Ramose, MJ; Fernandes, PA; Gameiro, P. "Combining theoretical and experimental approaches to understand the mechanism of antibiotic permeation: implications on the fight against bacterial resistance". 2019. Fernandes, P. "Multiscale QM/MM modelling and enzyme catalysis". 2010. Tamames, B; Fernandes, PA; Ramos, MJ. "HIV-1 Protease: a computational mutagenesis analysis of the monomers interface". 2009. Moura Tamames, SA; Ramos, MJ; Fernades, PA. "Exploring beta-1,3-Exoglucanase-polysaccharide interactions: molecular dynamics of the enzyme-substrate complex with or without a polysaccharide ligand bound in the flexible enzyme loops". 2009. Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ. "Enzyme Ribonucleotide Reductase. The Paradigm of Enzyme Inhibition by Furanone Derivatives". 2005. 10.1107/s0108767305079511
Conference paper	Almeida, Cristina F.; Augusto, Tiago V.; Oliveira, Ana; Correia-da-Silva, Georgina; Ramos, Maria João; Fernandes, Pedro Alexandrino; Teixeira, Natércia; Amaral, Cristina. "Tamoxifen bisphenol: a modulator of ERß in estrogen receptor-positive breast cancer". Trabalho apresentado em 6th International Electronic Conference on Medicinal Chemistry, 2020. Published • 10.3390/ECMC2020-07437 Almeida, Cristina; Oliveira, Ana; Fernandes, Pedro Alexandrino; Correia-da-Silva, Georgina; Ramos, Maria João; Augusto, Tiago V.; Teixeira, Natércia; Amaral, Cristina. "A novel approach for ER+ breast cancer treatment: A new compound that modulates aromatase and ER". Trabalho apresentado em 5th International Electronic Conference on Medicinal Chemistry, 2019. Published • 10.3390/ecmc2019-06337 Cristina F. Almeida; Augusto, Tiago V.; Correia-da-Silva, Georgina; Oliveira, Ana; Fernandes, Pedro Alexandrino; Ramos, Maria João; Cunha, Sara; Teixeira, Natércia. "Discovery of a multi-target compound for ER+ breast cancer: characterization of its biological effects". Trabalho apresentado em 14th YES - Young European Scientist - Meeting, Porto, 2019. Published • 10.1097/j.pbj.0000000000000054 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 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 MORADASFERREIRA, P; FERNANDES, PA; COSTA, MJ. "YEAST FLOCCULATION - THE ROLE OF CELL-WALL PROTEINS". 1994. 10.1016/0927-7765(94)80030-8
Conference poster	Castro-Amorim, Juliana; Alexandre V. Pinto; Ramos, Maria João; Fernandes, Pedro Alexandrino. Corresponding author: Castro-Amorim, Juliana. "On the intriguing world of snake venom toxins: Unravelling the catalytic pathway of phospholipase A2 toxin in a membrane model". Trabalho apresentado em 30th Meeting in Toxinology (RT30) of the SFET, Nice, France, 2024. Lima, Rita; Neves, Rui P. P.; Fernandes, Pedro Alexandrino; Silva, Artur; Tiritan, Maria Elizabeth; Pinto, Madalena M. M.; Fernandes, Carla. Corresponding author: Fernandes, Carla. "Predictive Computational Methods for Assessing Chiral Recognition Mechanisms on (S,S)-Whelk-O1® Column". Trabalho apresentado em 24th European Symposium on Quantitative Structure-Activity Relationship (24th EuroQSAR), 2024. Luís M. C. Teixeira; Paiva, Pedro; Fernandes, Pedro Alexandrino; Ramos, Maria João. Corresponding author: Ramos, Maria João. "Pseudomonas sp. MIS38 Lipase Potential for Urethane Biological Degradation". Trabalho apresentado em Enzymatic Polymer Degradation Symposium, 2024. Lima, Rita; Neves, Rui P. P.; Fernandes, Pedro Alexandrino; Silva, Artur; Tiritan, Maria Elizabeth; Pinto, Madalena M. M.; Fernandes, Carla. Corresponding author: Fernandes, Carla. "Computational approaches for chiral recognition mechanisms on (S,S)-Whelk-O1". Trabalho apresentado em 33rd International Symposium on Chirality, 2023. Malafaia, Daniela; Bras, Natercia F.; Fernandes, Pedro Alexandrino; Ramos, Maria; Silva, Artur; Albuquerque, Hélio. Corresponding author: Malafaia, Daniela. "Chromeno[3,4-b]xanthones: a new pathway towards the multitarget strategy for Alzheimer's disease". Trabalho apresentado em 22nd European Symposium on Organic Chemistry, 2023. Malafaia, Daniela; Bras, Natercia F.; Fernandes, Pedro Alexandrino; Ramos, Maria João; Silva, Artur; Albuquerque, Hélio. Corresponding author: Malafaia, Daniela. "Chromeno[3,4-b]xanthones: a new platform for the development of multitarget theranostics for Alzheimer's disease". Trabalho apresentado em Workshop on novel diagnostic tools for Alzheimer's disease, 2023. Pinto, Roberto; Fernandes, Pedro Alexandrino; Maria J. Ramos; Ferreira, Pedro G.. "New antidotes for the Bothrops asper venom: a study of PLA2 protein". Trabalho apresentado em 8th Portuguese Young Chemists Meeting (8th PYCheM), 2023. R. da Silva, Joana; Ana da Novo Oliveira; Ramos, Maria João; Fernandes, Pedro Alexandrino. Corresponding author: Fernandes, Pedro Alexandrino. "Uncovering the Structural Determinants of the sPLA2 Bothrops asper Viper’s Venom for Antidote Discovery Purposes". Trabalho apresentado em AIMS Meeting 2023, 2023. Proença, Carina; Rocha, Sónia; Freitas, Marisa; Fernandes, Pedro A.; Silva, Artur M. S.; Fernandes, Eduarda; Fernandes, Pedro Alexandrino; Eduarda Fernandes. "The effect of flavonoids and pyrazoles in the emerging targets of type 2 diabetes mellitus, PTP1B and FBPase". 2022. R. da Silva, Joana; Ana de Novo Oliveira; Ramos, Maria João; Fernandes, Pedro Alexandrino. Corresponding author: Fernandes, Pedro Alexandrino. "Discovery of Small-Molecule Antidotes for B. asper Viper’s Venom". Trabalho apresentado em 8th EUChemS Chemistry Congress 2022, 2022. R. da Silva, Joana; Ana de Novo Oliveira; Ramos, Maria João; Fernandes, Pedro Alexandrino. Corresponding author: Fernandes, Pedro Alexandrino. "Unveiling Structural Determinants for the Discovery of New Antidotes Against the B. asper Viper". Trabalho apresentado em Young Researchers of University of Porto Meeting (IJUP) 2022, 2022. Castro-Amorim, Juliana; Ana Luísa Novo de Oliveira; Ramos, Maria João; Fernandes, Pedro Alexandrino. "Revealing the enzymatic catalysis of Russell's viper venom factor X activator (RVV-X) using computational methods". Trabalho apresentado em VII Jornadas da Bioquímica, 2022. Proença, Carina; Freitas, Marisa; Rufino A.; de Oliveira, José Miguel P. Ferreira; Silva, Artur M. S.; Fernandes, Pedro Alexandrino; Fernandes, Eduarda. "Dual inhibition of carbohydrate-hydrolysing enzymes a-amylase and a-glucosidase by flavonoids". Trabalho apresentado em 14.º Encontro Nacional de Química Orgânica (14ENQO) e 7.º Encontro Nacional de Química Terapêutica (7ENQT), 2022. Proença, Carina; Rufino, A.T.; Ferreira de Oliveira, José Miguel P.; Fernandes, Pedro Alexandrino; Silva, Artur; Fernandes, Eduarda. "Evaluation of the Inhibitory Activity of Flavonoids on Sucrase-Isomaltase (a-Glucosidase) in a Caco-2/TC7 Cellular Model". Trabalho apresentado em RICT 2021 – 56th International Conference on Medicinal Chemistry, 2021. Paiva, Pedro; Ramos, Maria João; Fernandes, Pedro Alexandrino. "A computational study of the Fatty Acid Synthase: the catalytic mechanism of the Malonyl-Acetyl Transferase domain". Trabalho apresentado em 7th International Iberian Biophysics Congress, 2021. Castro-Amorim, Juliana; Ana Luísa Novo de Oliveira; Ramos, Maria João; Fernandes, Pedro Alexandrino. "Disclosing the molecular basis of substrate recognition of Russell's viper (Daboia russelii russelii) venom factor X activating enzyme (RVVX)". Trabalho apresentado em VII Jornadas da Bioquímica, 2021. Almeida, Cristina F.; Oliveira, Ana; Amaral, Cristina; Ramos, Maria João; Correia-da-Silva, Georgina; Teixeira, Natércia; Fernandes, Pedro Alexandrino. "A multi-target approach for hormone-dependent breast cancer: estrogen receptors and aromatase". Trabalho apresentado em Encontro de Jovens Investigadores de Biologia Computacional Estrutural, EJIBCE, 2018. Gesto, Diana S.; Özaydin, Beste; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. "From serotonin to melatonin - computational insights on the mechanism of serotonin N-acetyltransferase". Trabalho apresentado em International Conference on Catalysis Science, Engineering & Technology, 2018. Paiva, Pedro; Sérgio Filipe Maia de Sousa; Ramos, Maria João; Fernandes, Pedro Alexandrino. "A QM/MM study of human Malonyl-Acetyl Transferase". Trabalho apresentado em Dynapeutics International Summer School 2016, 2016. Gesto, Diana S.; Nuno, NMFSA; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. "Understanding the reaction mechanism of L-asparaginase II – a computational study". Trabalho apresentado em X Girona Seminar on Theoretical and Computational Chemistry for the Modeling of Biochemical Systems: From Theory to Applications, 2012. Gesto, Diana S.; Cerqueira, NMFSA; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. "Unveiling the Catalytic Mechanism of L-asparaginase II using Computational Methods". Trabalho apresentado em 3PYCheM - 3rd Portuguese Young Chemists Meeting, 2012. Gesto, Diana S.; Cerqueira, NMFSA; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. "Theoretical Insights on the Mechanism of L-asparaginase II". Trabalho apresentado em THEOBIO 2011 - 5th Symposium on Theoretical Biophysics, 2011. Gesto, Diana S.; Cerqueira, NMFSA; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. "Unraveling the Enigmatic Mechanism of Asparaginase: a Key Enzyme in the Battle against Cancer". Trabalho apresentado em 2o Encontro Nacional de Química Terapêutica, 2010. Gesto, Diana S.; Cerqueira, NMFSA; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. "Theoretical and Computational Studies addressed to Asparaginase". Trabalho apresentado em IJUP 2010 - 3rd Meeting of Young Researchers of U. Porto, 2010.
Journal article	Dev Madhubala; Rosy Mahato; Kangkon Saikia; Aparup Patra; Pedro Alexandrino Fernandes; Arun Kumar; Mojibur R. Khan; Ashis K. Mukherjee. "Snake Venom-Inspired Novel Peptides Protect Caenorhabditis elegans against Paraquat-Induced Parkinson’s Pathology". ACS Chemical Neuroscience (2025): https://doi.org/10.1021/acschemneuro.4c00576. 10.1021/acschemneuro.4c00576 Malthe Kjær Bendtsen; Jan Stanislaw Nowak; Pedro Paiva; Marcos López Hernández; Pedro Ferreira; Jan Skov Pedersen; Nicolai Sundgaard Bekker; et al. "Cold-Active Starch-Degrading Enzymes from a Cold and Alkaline Greenland Environment: Role of Ca²⁺ Ions and Conformational Dynamics in Psychrophilicity". Biomolecules (2025): https://www.mdpi.com/2218-273X/15/3/415. 10.3390/biom15030415 Christian Gusenda; Ana R. Calixto; Joana R. Da Silva; Pedro A. Fernandes; Martin Grininger. "Die Kinetik der Kohlenstoff-Kohlenstoff-Bindungsbildung in der metazoischen Fettsäure Synthase und ihr Einfluss auf die Produktgenauigkeit". Angewandte Chemie (2025): https://doi.org/10.1002/ange.202412195. 10.1002/ange.202412195 Christian Gusenda; Ana R. Calixto; Joana R. Da Silva; Pedro A. Fernandes; Martin Grininger. "The Kinetics of Carbon-Carbon Bond Formation in Metazoan Fatty Acid Synthase and Its Impact on Product Fidelity". Angewandte Chemie International Edition (2025): https://doi.org/10.1002/anie.202412195. 10.1002/anie.202412195 Joana R. da Silva; Maria João Ramos; Pedro A. Fernandes. "Elucidating on the quaternary structure of viper venom phospholipase A2 enzymes in aqueous solution". Biochimie (2025): https://doi.org/10.1016/j.biochi.2024.12.015. 10.1016/j.biochi.2024.12.015 João P. M. Sousa; Maria J. Ramos; Pedro A. Fernandes. "The Catalytic Mechanism of Decarboxylation of L-DOPA to Dopamine by Papaver somniferum Aromatic Amino Acid Decarboxylase – A Computational Study". ChemCatChem (2025): https://doi.org/10.1002/cctc.202400762. 10.1002/cctc.202400762 P. Paiva; E. Ippoliti; P. Carloni; P. A. Fernandes; M. J. Ramos. "Atomistic adsorption of PETase onto large-scale PET 3D-models that mimic reality". Physical Chemistry Chemical Physics (2025): https://doi.org/10.1039/D4CP03488K. 10.1039/D4CP03488K Juliana Castro-Amorim; Alexandre V. Pinto; Ashis K. Mukherjee; Maria J. Ramos; Pedro A. Fernandes. "Beyond Fang's fury: a computational study of the enzyme–membrane interaction and catalytic pathway of the snake venom phospholipase A2 toxin". Chemical Science (2025): https://doi.org/10.1039/D4SC06511E. 10.1039/D4SC06511E Paiva, Pedro; Correia Teixeira, Luís Miguel; Ren, Wei; Liu, Weidong; Weber, Gert; Morth, Jens Preben; Westh, Peter; et al. "Unveiling the Enzymatic Pathway of UMG-SP2 Urethanase: Insights into Polyurethane Degradation at the Atomic Level". Chemical Science (2025): https://doi.org/10.1039/d4sc06688j. 10.1039/d4sc06688j Beatriz T. Magalhães; João T. S. Coimbra; Raquel M. Silva; Mariana Ferreira; Rita S. Santos; Paula Gameiro; Nuno F. Azevedo; Pedro A. Fernandes. "Crosstalk of Nucleic Acid Mimics with Lipid Membranes: A Multifaceted Computational and Experimental Study". Biochemistry (2024): https://doi.org/10.1021/acs.biochem.4c00349. 10.1021/acs.biochem.4c00349 João T. S. Coimbra; Antoine Gissler; Emiel Nitor; Kiana Rostamipour; Ana V. Cunha; Maria J. Ramos; Pedro A. Fernandes. "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2-like Peptides". JACS Au (2024): https://doi.org/10.1021/jacsau.4c00646. 10.1021/jacsau.4c00646 João P. M. Sousa; Maria J. Ramos; Pedro A. Fernandes. "QM/MM Study of the Reaction Mechanism of L-Tyrosine Hydroxylation Catalyzed by the Enzyme CYP76AD1". The Journal of Physical Chemistry B (2024): https://doi.org/10.1021/acs.jpcb.4c05209. 10.1021/acs.jpcb.4c05209 Coelho, Maria Miguel; Lima, Rita; Almeida, Ana Sofia; Fernandes, Pedro Alexandrino; Remião, Fernando; Fernandes, Carla; Tiritan, Maria Elizabeth. Corresponding author: Fernandes, Carla. "Binding studies of promethazine and its metabolites with human serum albumin by high performance affinity chromatography and molecular docking in the presence of codeine". Analytical and Bioanalytical Chemistry (2024): Published Ali, Mohd Sajid; Luís M. C. Teixeira; Ramos, Maria João; Fernandes, Pedro Alexandrino; Al-Lohedan, Hamad A.. "Interaction of major saffron constituent safranal with trypsin: An experimental and computational investigation". International Journal of Biological Macromolecules (2024): http://dx.doi.org/10.1016/j.ijbiomac.2024.133231. 10.1016/j.ijbiomac.2024.133231 Pedro Ferreira; Rui P. P. Neves; Filipa P. Miranda; Ana V. Cunha; Remco W. A. Havenith; Maria J. Ramos; Pedro A. Fernandes. "DszA Catalyzes C–S Bond Cleavage through N5–Hydroperoxyl Formation". Journal of Chemical Information and Modeling (2024): https://doi.org/10.1021/acs.jcim.4c00301. 10.1021/acs.jcim.4c00301 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 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 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 Boro, N; Fernandes, PA; Mukherjee, AK. "Computational analysis to comprehend the structure-function properties of fibrinolytic enzymes from Bacillus spp for their efficient integration into industrial applications". HELIYON (2024): https://www.authenticus.pt/P-010-YST. 10.1016/j.heliyon.2024.e33895 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 "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 "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 "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 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 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 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 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 Ferreira, P; Fernandes, PA; Ramos, MJ. "Modern computational methods for rational enzyme engineering". CHEM CATALYSIS (2022): https://www.authenticus.pt/P-00X-D5M. 10.1016/j.checat.2022.09.036 Amaral, LMPF; Moniz, T; Leite, A; Oliveira, A; Fernandes, P; Ramos, MJ; Araujo, AN; et al. "A combined experimental and computational study to discover novel tyrosinase inhibitors". JOURNAL OF INORGANIC BIOCHEMISTRY (2022): https://www.authenticus.pt/P-00W-PVQ. 10.1016/j.jinorgbio.2022.111879 Perrin, CL; Agranat, I; Bagno, A; Braslavsky, SE; Fernandes, PA; Gal, JF; Lloyd-Jones, GC; et al. "Glossary of terms used in physical organic chemistry (IUPAC Recommendations 2021)". PURE AND APPLIED CHEMISTRY (2022): https://www.authenticus.pt/P-00W-QNK. 10.1515/pac-2018-1010 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 Pedro Fernandes; Francisco Félix. "“Tão natural”". Revista de Ciência Elementar (2021): https://doi.org/10.24927/rce2021.072. 10.24927/rce2021.072 "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 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 "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 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 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 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 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 "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 "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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Pedro Fernandes. "A Ciência é a única arma". Revista de Ciência Elementar (2020): https://doi.org/10.24927/rce2020.017. 10.24927/rce2020.017 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 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 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 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 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 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 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 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 Fernandes, Pedro. "The Catalytic Mechanism of Human Transketolase". ChemPhysChem (2019): http://dx.doi.org/10.1002/cphc.201900650. 10.1002/cphc.201900650 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 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 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 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 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 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 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 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 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 Gameiro, P.; Sousa, C. F.; Coimbra, J. T. S.; Fernandes, P. A.; Ramos, M. J.. "Drug Permeation Across the Bacterial Membrane: Combining Theoretical and Experimental Approaches". Biophysical Journal 116 3 (2019): 206A-206A. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000460779801038&KeyUID=WOS:000460779801038. 10.1016/j.bpj.2018.11.1138 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Pedro Fernandes; Ana Calixto. "Moléculas magníficas". Revista de Ciência Elementar 5 2 (2017): https://doi.org/10.24927%2Frce2017.027. 10.24927/rce2017.027 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 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 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. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Ferreira, P; Sousa, SF; Fernandes, PA; Ramos, MJ. "Frontispiece: Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives". Chemistry – A European Journal (2017): https://www.authenticus.pt/P-00Z-K6H. 10.1002/chem.201786864 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Pedro Fernandes. "Prémio Casa das Ciências". Revista de Ciência Elementar 3 3 (2015): https://doi.org/10.24927/rce2015.037. 10.24927/rce2015.037 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Gesto, D.S.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Gemcitabine: A critical nucleoside for cancer therapy". Current Medicinal Chemistry 19 7 (2012): 1076-1087. http://www.scopus.com/inward/record.url?eid=2-s2.0-84858173640&partnerID=MN8TOARS. 10.2174/092986712799320682 Salome, PMP; Malaquias, J; Fernandes, PA; Ferreira, MS; da Cunha, AF; Leitao, JP; Gonzalez, JC; Matinaga, FM. "Growth and characterization of Cu2ZnSn(S,Se)(4) thin films for solar cells". SOLAR ENERGY MATERIALS AND SOLAR CELLS (2012): https://www.authenticus.pt/P-002-9SV. 10.1016/j.solmat.2012.02.031 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 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 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 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 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 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 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. 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 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 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 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 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 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 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 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 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 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 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 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 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 Rodriguez, E; Azevedo, R; Fernandes, P; Santos, C. "Cr(VI) Induces DNA Damage, Cell Cycle Arrest and Polyploidization: A How Cytometric and Comet Assay Study in Pisum sativum". CHEMICAL RESEARCH IN TOXICOLOGY (2011): https://www.authenticus.pt/P-002-Q1A. 10.1021/tx2001465 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Cerqueira, N.M.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Virtual screening of compound libraries.". Methods in molecular biology (Clifton, N.J.) 572 (2009): 57-70. http://www.scopus.com/inward/record.url?eid=2-s2.0-79952110876&partnerID=MN8TOARS. 10.1007/978-1-60761-244-5_4 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. 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. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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. 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. 10.1021/jp993045z Falcao Moreira, R; Ferreira Da Silva, F; Fernandes, PA; Moradas Ferreira, P. "Flocculation of Saccharomyces cerevisiae is induced by transformation with the GAP1 gene from Kluyveromyces marxianus". YEAST (2000): https://www.authenticus.pt/P-001-105. 10.1002/(sici)1097-0061(200002)16:3<231::aid-yea530>3.0.co;2-c 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. 10.1021/jp9844213 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. 10.1021/jp983170v 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 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 Moreira, RF; Fernandes, PA; Moradas Ferreira, P. "Kluyveromyces marxianus flocculence and growth at high temperature is dependent on the presence of the protein p37". MICROBIOLOGY-UK (1998): https://www.authenticus.pt/P-001-8DC. 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. 10.1063/1.470554 FERNANDES, PA; SENAESTEVES, M; MORADASFERREIRA, P. "CHARACTERIZATION OF THE GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE GENE FAMILY FROM KLUYVEROMYCES-MARXIANUS - POLYMERASE CHAIN REACTION-SINGLE-STRAND CONFORMATION POLYMORPHISM AS A TOOL FOR THE STUDY OF MULTIGENIC FAMILIES". YEAST (1995): https://www.authenticus.pt/P-001-GQV. 10.1002/yea.320110804 FERNANDES, PA; SOUSA, M; MORADASFERREIRA, P. "FLOCCULATION OF KLUYVEROMYCES-MARXIANUS IS INDUCED BY A TEMPERATURE UPSHIFT". YEAST (1993): https://www.authenticus.pt/P-001-MVM. 10.1002/yea.320090806 FERNANDES, PA; KEEN, JN; FINDLAY, JBC; MORADASFERREIRA, P. "A PROTEIN HOMOLOGOUS TO GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IS INDUCED IN THE CELL-WALL OF A FLOCCULANT KLUYVEROMYCES-MARXIANUS". BIOCHIMICA ET BIOPHYSICA ACTA (1992): https://www.authenticus.pt/P-001-P6B. 10.1016/0167-4838(92)90076-p
Preprint	Pinto, AV; Ferreira, P; Cunha, AV; Havenith, RWA; Magalhaes, AL; Ramos, MJ; Fernandes, PA. "Revisiting the reaction pathways for phospholipid hydrolysis catalyzed by phospholipase A2 with QM/MM methods". 2024. https://www.authenticus.pt/P-010-HSR. 10.1039/d4sc02315c Christian Gusenda; Ana Rita Calixto; Joana Margarida Ribeiro da Silva; Pedro Alexandrino Fernandes; Martin Grininger. "The Kinetics of Carbon-Carbon-Bond Formation in Metazoan Fatty Acid Synthase and its Impact on Product Fidelity". 2024. https://doi.org/10.1101/2024.07.03.601458. 10.1101/2024.07.03.601458 Pimenta das Neves, RP; Viveiros Araújo, BM; Ramos, MJ; Fernandes, PA. "Feedback inhibition of DszC, a crucial enzyme for crude oil biodessulfurization". 2023. https://www.authenticus.pt/P-00Y-1C9. 10.26434/chemrxiv-2023-fxdp0

Other

Annotation	de Oliveira, L; Lacerda, T; Ramos, J; Fernandes, A. 2024. "Correction to: Viper Venom Phospholipase A2 Database: The Structural and Functional Anatomy of a Primary Toxin in Envenomation (Toxins, (2024), 16, 2, (71), 10.3390/toxins16020071)". 10.3390/toxins16060250
Dataset	Coimbra, João TS; Fernandes, Pedro Alexandrino; Ramos, Maria João. Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations". Zenodo. 2023. https://doi.org/10.5281/zenodo.8255787
Other output	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

Oral presentation

	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.

Supervision

	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 Supervisor

Jury of academic degree

	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 (Other)

Committee member

	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.

Conference scientific committee

	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.

Consulting

	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).

Course / Discipline taught

	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.

Evaluation committee

	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) Evaluator		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

Journal scientific committee

	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

Distinções

Award

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

Title

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

Other distinction

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