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Identificação

Identificação pessoal

Nome completo
Maria João Ramos
Género
Feminino

Nomes de citação

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

Identificadores de autor

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

Endereços de correio eletrónico

  • mjramos@fc.up.pt (Profissional)

Domínios de atuação

  • Ciências Exatas - Química
  • Ciências Naturais - Ciências Biológicas - Bioquímica
  • Ciências Exatas - Ciências da Computação e da Informação - Bioinformática
Formação
Grau Classificação
2014/09/30
Concluído
 Honorary Doctorate (Doctor)
Stockholms Universitet, Suécia
2000
Concluído
 Chemistry (Título de Agregado)
Universidade do Porto Faculdade de Ciências, Portugal
1991
Concluído
 Chemistry (Pós-doutoramento)
University of Oxford, Reino Unido
1983
Concluído
 Chemistry (Doutoramento)
University of Glasgow, Reino Unido
1977
Concluído
 Chemistry (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal
Percurso profissional

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento 		Empregador
2010 - Atual Professor Catedrático (Docente Universitário) Universidade do Porto Faculdade de Ciências, Portugal
1989 - 2010 Professor Associado (Docente Universitário) Universidade do Porto Faculdade de Ciências, Portugal
1984 - 1989 Professor Auxiliar (Docente Universitário) Universidade do Porto Faculdade de Ciências, Portugal
1979 - 1984 Assistente (Docente Universitário) Universidade do Porto Faculdade de Ciências, Portugal

Cargos e Funções

Categoria Profissional
Instituição de acolhimento 		Empregador
2014/06/27 - 2018/06/27 Vice-Reitor Universidade do Porto, Portugal
2014/06/27 - 2018/06/27 Diretor UPTEC Associação de Transferência de Tecnologia da Asprela, Portugal
2009/03/25 - 2012/03/25 President of Department Universidade do Porto Faculdade de Ciências, Portugal
2000 - 2010 Associate Director National Foundation for Cancer Research, Estados Unidos
Projetos

Bolsa

Designação Financiadores
2022/12/18 - 2028/12/18 Center for enzymatic deconstruction of thermoset plastics for a sustainable society
DKK 57,003,755
PI in Portugal
Novo Nordisk Fonden, Dinamarca
Em curso

Projeto

Designação Financiadores
2019 - 2020 Bacterial Initiation factors and Termination factors as new targets to novel antibiotics
2018184467
2018184467
Investigador responsável
Universidade do Porto Faculdade de Ciências, Portugal
 Partnership for Advanced Computing In Europe
Concluído
2019 - 2020 Local and collective motions as a gateway to the catalytic power of enzymes
CHM150-2019
CHM150-2019
Investigador responsável
Universidade do Porto Faculdade de Ciências, Portugal
 Oak Ridge National Laboratory
Concluído
2018 - 2020 New biocatalysts for green crude oil desulfurization
PTDC/QUI-QFI/28714/2017
PTDC/QUI-QFI/28714/2017
Investigador
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2015 - 2020 TCCM - Theoretical Chemistry and Computational Modelling
ITN-EJD-642294
Investigador responsável
Universidade do Porto Faculdade de Ciências, Portugal
 European Union
Concluído
2016 - 2019 New Technologies for three Health Challenges of Modern Societies: Diabetes, Drug Abuse and Kidney Diseases
NORTE-01-0145-FEDER-000024
Investigador responsável
REQUIMTE LAQV Porto, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Concluído
2015 - 2019 NatChemDrugs - Challenging Organic Syntheses Inspired by Nature: from Natural Products Chemistry to Drug Discovery
European Project CM1407
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 European Union
Concluído
2014 - 2019 Aldehyde Oxidases in Drug Metabolism and Biocatalysis: Searching for the Substrate Specificity and Catalytic Mechanism
PTDC/BBB-BEP/1185/2014
PTDC/BBB-BEP/1185/2014
Investigador
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2013/01/01 - 2018 ENZYMATIC CATALYSIS - seeking a global picture
info:eu-repo/grantAgreement/FCT/COMPETE/128544/PT
Investigador responsável
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2013 - 2015 Chelators for novel therapeutic strategies
NORTE-07-0124-FEDER-000066
NORTE-07-0124-FEDER-000066
Investigador
REQUIMTE LAQV Porto, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Concluído
2012/05/01 - 2014 New drugs for hypertension
info:eu-repo/grantAgreement/FCT/COMPETE/121744/PT
Investigador responsável
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2010 - 2014 CODECS: COnvergent Distributed Environment for Computational Spectroscopy
European Project oc-2009-2-5734
European Project oc-2009-2-5734
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 European Union
Concluído
2010 - 2014 Molecular machineries for ion translocation across biomembranes
European Project CM0902
European Project CM0902
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 N/A
Concluído
2010 - 2014 Developing on-the-fly quantum dynamics for proton transfer in enzyme catalysis
Leverhulm Trust
Investigador
Concluído
2010 - 2013 An innovative methodology to calculate drug-receptor binding free energies
PTDC/QUI-QUI/100372/2008
PTDC/QUI-QUI/100372/2008
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2010 - 2012 Molecular Mechanisms of Hypercholesterolemia: New insights and New Therapeutic Strategies
PTDC/QUI-QUI/102760/2008
Investigador
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2010 - 2012 New Biomolecular Force Field
PTDC/QUI-QUI/103118/2008
PTDC/QUI-QUI/103118/2008
Investigador responsável
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2009/01/02 - 2011 Novel Key Molecular Architectures to Target Infection
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/67915/PT
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2008 - 2010 Drug design towards the HIV-1 virus
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/68302/PT
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2008 - 2010 Uma abordagem complementar por Cristalografia de Raios-X, RMN e Química Computacional para a compreensão dos mecanismos de reconhecimento e ligação de substratos em módulos proteicos de ligação a polissacáridos
PTDC/QUI/68286/2006
PTDC/QUI/68286/2006
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2008 - 2010 Estudos Espectroscópicos e Computacionais do Mecanismo Catalítico da Redutase do Nitrato
PTDC/QUI/67052/2006
PTDC/QUI/67052/2006
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2005 - 2008 Catálise Enzimática: Estudos Mecanísticos de Enzimas Humanas Relacionadas com o Processo Cancerígeno
POCTI/QUI/61563/2004
Investigador responsável
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2005 - 2008 MODELAÇÃO MOLECULAR E SÍNTESE DE PÉPTIDOS BIOACTIVOS
POCTI/QUI/55673/2004
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2006 - 2007 Comparative Binding Energy Studies on Balanol Analogues As Inhibitors of Cyclic-AMP Dependent Protein Kinase: Development of HIV-Gene Expression Inhibitors By Targeting the Activation of Nuclear Factor – Kappa B
Luso-Spanish Agreement NºE-26/06
Investigador responsável
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2004 - 2007 Infraestrutura de Cálculo Paralelo de Alta Performance para Química Computacional no Laboratório Associado REQUIMTE
CONC-REEQ/1236/2001
CONC-REEQ/1236/2001
Investigador responsável
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
1998 - 2005 Estudo teórico do comportamento de ácidos monopróticos em solventes mistos água/álcool
PRAXIS/P/QUI/11302/98
PRAXIS/P/QUI/11302/98
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2000 - 2003 Modelação de Mecanismos de Inibição em Radicais Enzimáticos: Uma proposta QM/CM
POCTI/35376/QUI/2000
POCTI/35376/QUI/2000
Investigador responsável
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
1996 - 2002 Estudos de Adsorção sobre Superfícies Metálicas: uma Abordagem Teórica
PRAXIS/PCEX/C/QUI/61/96
PRAXIS/PCEX/C/QUI/61/96
Investigador
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído

Outro

Designação Financiadores
2020 - 2023 Murderous Venom - towards a universal antidote against snakebite
PTDC/QUI-OUT/1401/2020
co-PI
REQUIMTE LAQV Porto, Portugal
2018/01/01 - 2021/12/31 NEW BIOCATALYSTS FOR GREEN CRUDE OIL DESULFURIZATION
PTDC/QUI-QFI/28714/2017
Co-PI
REQUIMTE LAQV Porto, Portugal

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

Publicações

Artigo em conferência
  1. Brito, NT; Ramos, MJ. "On-line classroom, a way of collecting information about students' skills". 2004.
Artigo em revista
  1. Amaral, LMPF; Moniz, T; Leite, A; Oliveira, A; Fernandes, P; Ramos, MJ; Araujo, AN; et al. "A combined experimental and computational study to discover novel tyrosinase inhibitors". JOURNAL OF INORGANIC BIOCHEMISTRY (2022):
    10.1016/j.jinorgbio.2022.111879
  2. Neves, RPP; Cunha, AV; Fernandes, PA; Ramos, MJ. "Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms". CHEMPHYSCHEM (2022):
    10.1002/cphc.202200159
  3. Viegas, MF; Neves, RPP; Ramos, MJ; Fernandes, PA. "QM/MM Study of the Reaction Mechanism of Thermophilic Glucuronoyl Esterase for Biomass Treatment". CHEMPHYSCHEM (2022):
    10.1002/cphc.202200269
  4. Coimbra, JTS; Neves, RPP; Cunha, AV; Ramos, MJ; Fernandes, PA. "Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease". CHEMISTRY-A EUROPEAN JOURNAL (2022):
    10.1002/chem.202201066
  5. Teixeira, LMC; Coimbra, JTS; Ramos, MJ; Fernandes, PA. "Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic". JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022):
    10.1021/acs.jcim.1c01561
  6. Sousa, CF; Coimbra, JTS; Richter, R; Morais-Cabral, JH; Ramos, MJ; Lehr, CM; Fernandes, PA; Gameiro, P. "Exploring the permeation of fluoroquinolone metalloantibiotics across outer membrane porins by combining molecular dynamics simulations and a porin-mimetic in vitro model". BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2022):
    10.1016/j.bbamem.2021.183838
  7. Neves, RPP; Ramos, MJ; Fernandes, PA. "Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis". JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022):
    10.1021/acs.jcim.2c01337
  8. Pinto, AV; Ferreira, P; Fernandes, PA; Magalhaes, AL; Ramos, MJ. "Development of Nanoscale Graphene Oxide Models for the Adsorption of Biological Molecules". JOURNAL OF PHYSICAL CHEMISTRY B (2022):
    10.1021/acs.jpcb.2c06037
  9. Neves, RPP; Fernandes, PA; Ramos, MJ. "Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by alpha-Amylase Explored with QM/MM Molecular Dynamics". JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022):
    10.1021/acs.jcim.2c00691
  10. Fernandes, PA; Passos, O; Ramos, MJ. "Necessity is the Mother of Invention: A Remote MolecularBioinformatics Practical Course in the COVID-19 Era br". JOURNAL OF CHEMICAL EDUCATION (2022):
    10.1021/acs.jchemed.1c01195
  11. Almeida, Cristina Ferreira; Teixeira, Natércia; Oliveira, Ana; Augusto, Tiago V.; Correia-da-Silva, Georgina; Ramos, Maria João; Fernandes, Pedro Alexandrino; Amaral, Cristina. "Discovery of a multi-target compound for estrogen receptor-positive (ER+) breast cancer: Involvement of aromatase and ERs". Biochimie 181 (2021): 65-76. http://dx.doi.org/10.1016/j.biochi.2020.11.023.
    10.1016/j.biochi.2020.11.023
  12. Brás, Natércia F.; Ferreira, Pedro; Calixto, Ana R.; Jaspars, Marcel; Houssen, Wael; Naismith, James H.; Fernandes, Pedro A.; Ramos, Maria J.. "Corrigendum: The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac". Chemistry – A European Journal 27 10 (2021): 3569-3569. http://dx.doi.org/10.1002/chem.202100062.
    10.1002/chem.202100062
  13. Coimbra, João T. S.; Feghali, Ralph; Ribeiro, Rui P.; Ramos, Maria J.; Fernandes, Pedro A.. "The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer". RSC Advances 11 2 (2021): 899-908. http://dx.doi.org/10.1039/d0ra09995c.
    10.1039/d0ra09995c
  14. Jerves, C; Neves, RPP; Ramos, MJ; da Silva, S; Fernandes, PA. "Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations". ACS CATALYSIS (2021):
    10.1021/acscatal.1c03700
  15. Ong, HC; Coimbra, JTS; Kwek, G; Ramos, MJ; Xing, BA; Fernandes, PA; Garcia, F. "Alkyl vs. aryl modifications: a comparative study on modular modifications of triphenylphosphonium mitochondrial vectors". RSC CHEMICAL BIOLOGY (2021):
    10.1039/d1cb00099c
  16. Neves, RPP; Ferreira, P; Medina, FE; Paiva, P; Sousa, JPM; Viegas, MF; Fernandes, PA; Ramos, MJ. "Engineering of PKS Megaenzymes-A Promising Way to Biosynthesize High-Value Active Molecules". TOPICS IN CATALYSIS (2021):
    10.1007/s11244-021-01490-5
  17. Bras, NF; Neves, RPP; Lopes, FAA; Correia, MAS; Palma, AS; Sousa, SF; Ramos, MJ. "Combined in silico and in vitro studies to identify novel antidiabetic flavonoids targeting glycogen phosphorylase". BIOORGANIC CHEMISTRY (2021):
    10.1016/j.bioorg.2020.104552
  18. Sousa, CF; Coimbra, JTS; Ferreira, M; Pereira Leite, C; Reis, S; Ramos, MJ; Fernandes, PA; Gameiro, P. "Passive Diffusion of Ciprofloxacin and its Metalloantibiotic: A Computational and Experimental study". JOURNAL OF MOLECULAR BIOLOGY (2021):
    10.1016/j.jmb.2021.166911
  19. Pinto, AV; Ferreira, P; Neves, RPP; Fernandes, PA; Ramos, MJ; Magalhaes, AL. "Reaction Mechanism of MHETase, a PET Degrading Enzyme". ACS CATALYSIS (2021):
    10.1021/acscatal.1c02444
  20. Ferreira, P; Cerqueira, NMFSA; Fernandes, PA; Romao, MJ; Ramos, MJ. "Catalytic Mechanism of Human Aldehyde Oxidase". ACS CATALYSIS (2020):
    10.1021/acscatal.0c02627
  21. Sousa, JPM; Neves, RPP; Sousa, SF; Ramos, MJ; Fernandes, PA. "Reaction Mechanism and Determinants for Efficient Catalysis by DszB, a Key Enzyme for Crude Oil Bio-desulfurization". ACS CATALYSIS (2020):
    10.1021/acscatal.0c03122
  22. Proenca, C; Oliveira, A; Freitas, M; Ribeiro, D; Sousa, JLC; Ramos, MJ; Silva, AMS; Fernandes, PA; Fernandes, E. "Structural Specificity of Flavonoids in the Inhibition of Human Fructose 1,6-Bisphosphatase". JOURNAL OF NATURAL PRODUCTS (2020):
    10.1021/acs.jnatprod.0c00014
  23. Sousa, SF; Calixto, AR; Ferreira, P; Ramos, MJ; Lim, C; Fernandes, PA. "Activation Free Energy, Substrate Binding Free Energy, and Enzyme Efficiency Fall in a Very Narrow Range of Values for Most Enzymes". ACS CATALYSIS (2020):
    10.1021/acscatal.0c01947
  24. Prejano, M; Medina, FE; Ramos, MJ; Russo, N; Fernandes, PA; Marino, T. "How the Destabilization of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase". ACS CATALYSIS (2020):
    10.1021/acscatal.9b04690
  25. Almada, M; Amaral, C; Oliveira, A; Fernandes, PA; Ramos, MJ; Fonseca, BM; Correia da Silva, G; Teixeira, N. "Cannabidiol (CBD) but not tetrahydrocannabinol (THC) dysregulate in vitro decidualization of human endometrial stromal cells by disruption of estrogen signaling". REPRODUCTIVE TOXICOLOGY (2020):
    10.1016/j.reprotox.2020.01.003
  26. Paiva, P; Ramos, MJ; Fernandes, PA. "Assessing the validity ofDLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions". JOURNAL OF COMPUTATIONAL CHEMISTRY (2020):
    10.1002/jcc.26401
  27. Sousa, R; Moorthy, NSHN; Fernandes, PA; Ramos, MJ; Bras, NF. "Binding Mode Prediction and Identification of New Lead Compounds from Natural Products as 3-OST Enzyme Inhibitors". LETTERS IN DRUG DESIGN & DISCOVERY (2020):
    10.2174/1570180817666200313105944
  28. Teixeira, CSS; Ramos, MJ; Sousa, SF; Cerqueira, NMFSA. "Solving the Catalytic Mechanism of Tryptophan Synthase: an Emergent Drug Target in the Treatment of Tuberculosis". CHEMCATCHEM (2020):
    10.1002/cctc.201901505
  29. 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
  30. Proenca, C.; Freitas, M.; Ribeiro, D.; Tome, S. M.; Oliveira, E. F. T.; Viegas, M. F.; Araujo, A. N.; et al. "Evaluation of a flavonoids library for inhibition of pancreatic alpha-amylase towards a structure-activity relationship". Journal of Enzyme Inhibition and Medicinal Chemistry 34 1 (2019): 577-588. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000457961100001&KeyUID=WOS:000457961100001.
    10.1080/14756366.2018.1558221
  31. 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
  32. Puzzarini, C.; de Lara-Castells, M. P.; Ramos, M. J.. "Challenges in spectroscopy: accuracy versus interpretation from isolated molecules to condensed phases". Physical Chemistry Chemical Physics 21 7 (2019): 3395-3396. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000459585900001&KeyUID=WOS:000459585900001.
    10.1039/c9cp90025j
  33. Ribeiro, J; Branco, MC; Ribeiro, JA. "The corporatisation of football and CSR reporting by professional football clubs in Europe". INTERNATIONAL JOURNAL OF SPORTS MARKETING & SPONSORSHIP (2019):
    10.1108/ijsms-05-2017-0039
  34. dos Santos Moreira, CDD; Ribeiro Nunes Ramos, MJRN; Azevedo Alexandrino Fernandes, PMAA. "Glutamine synthetase structure-catalysis relationship-Recent advances and applications". WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2019):
    10.1002/wcms.1399
  35. Coimbra, JTS; Bras, NF; Fernandes, PA; Rangel, M; Ramos, MJ. "A computational study on the redox properties and binding affinities of iron complexes of hydroxypyridinones". JOURNAL OF MOLECULAR MODELING (2019):
    10.1007/s00894-019-4037-0
  36. Dalla Torre, G; Mujika, JI; Izabela Lachowicz, JI; Ramos, MJ; Lopez, X. "The interaction of aluminum with catecholamine-based neurotransmitters: can the formation of these species be considered a potential risk factor for neurodegenerative diseases?". DALTON TRANSACTIONS (2019):
    10.1039/c8dt04216k
  37. Ribeiro, J; Davids, K; Araujo, D; Silva, P; Ramos, J; Lopes, R; Garganta, J. "The Role of Hypernetworks as a Multilevel Methodology for Modelling and Understanding Dynamics of Team Sports Performance". SPORTS MEDICINE (2019):
    10.1007/s40279-019-01104-x
  38. Araujo, MP; Nunes, M; Rocha, IM; Pereira, MFR; Freire, C. "Electrocatalytic activity of new Mn3O4@oxidized graphene flakes nanocomposites toward oxygen reduction reaction". JOURNAL OF MATERIALS SCIENCE (2019):
    10.1007/s10853-019-03508-6
  39. Almada, M; Oliveira, A; Amaral, C; Fernandes, PA; Ramos, MJ; Fonseca, B; Correia da Silva, G; Teixeira, N. "Anandamide targets aromatase: A breakthrough on human decidualization". BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS (2019):
    10.1016/j.bbalip.2019.08.008
  40. Calixto, AR; Ramos, MJ; Fernandes, PA. "Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway". CHEMICAL SCIENCE (2019):
    10.1039/c9sc01464k
  41. Ferreira, P; Cerqueira, NMFSA; Coelho, C; Fernandes, PA; Romao, MJ; Ramos, MJ. "New insights about the monomer and homodimer structures of the human AOX1". PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2019):
    10.1039/c9cp01040h
  42. Ong, HC; Hu, Z; Coimbra, JTS; Ramos, MJ; Kon, OL; Xing, BG; Yeow, EKL; Fernandes, PA; Garcia, F. "Enabling Mitochondrial Uptake of Lipophilic Dications Using Methylated Triphenylphosphonium Moieties". INORGANIC CHEMISTRY (2019):
    10.1021/acs.inorgchem.8b03380
  43. Listyarini, RV; Gesto, DS; Paiva, P; Ramos, MJ; Fernandes, PA. "Benchmark of Density Functionals for the Calculation of the Redox Potential of Fe3+/Fe2+ Within Protein Coordination Shells". FRONTIERS IN CHEMISTRY (2019):
    10.3389/fchem.2019.00391
  44. Medina, FE; Ramos, MJ; Fernandes, PA. "Complexities of the Reaction Mechanisms of CC Double Bond Reduction in Mammalian Fatty Acid Synthase Studied with Quantum Mechanics/Molecular Mechanics Calculations". ACS CATALYSIS (2019):
    10.1021/acscatal.9b03531
  45. Prejano, M; Medina, FE; Fernandes, PA; Russo, N; Ramos, MJ; Marino, T. "The Catalytic Mechanism of Human Transketolase". CHEMPHYSCHEM (2019):
    10.1002/cphc.201900650
  46. Paiva, P; Sousa, SF; Fernandes, PA; Ramos, MJ. "Human Fatty Acid Synthase: A Computational Study of the Transfer of the Acyl Moieties from MAT to the ACP Domain". CHEMCATCHEM (2019):
    10.1002/cctc.201900548
  47. Fernandes, H. S.; Ramos, M. J.; Cerqueira, Nmfsa. "Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study". Acs Catalysis 8 11 (2018): 10096-10110. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000449723900021&KeyUID=WOS:000449723900021.
    10.1021/acscatal.8b02321
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. Simoes, I. C. M.; Coimbra, J. T. S.; Neves, R. P. P.; Costa, I. P. D.; Ramos, M. J.; Fernandes, P. A.. "Properties that rank protein: protein docking poses with high accuracy". Physical Chemistry Chemical Physics 20 32 (2018): 20927-20942. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000447367900018&KeyUID=WOS:000447367900018.
    10.1039/c8cp03888k
  55. 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
  56. Fernandes, H. S.; Ramos, M. J.; Cerqueira, Nmfsa. "molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software". Journal of Computational Chemistry 39 19 (2018): 1344-1353. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000434970500019&KeyUID=WOS:000434970500019.
    10.1002/jcc.25189
  57. Zuniga, M. A.; Alderete, J. B.; Jana, G. A.; Fernandez, P. A.; Ramos, M. J.; Jimenez, V. A.. "Modulation of lateral and longitudinal interdimeric interactions in microtubule models by Laulimalide and Peloruside A association: A molecular modeling approach on the mechanism of microtubule stabilizing agents". Chemical Biology & Drug Design 91 5 (2018): 1042-1055. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000430168300006&KeyUID=WOS:000430168300006.
    10.1111/cbdd.13168
  58. Gabriele Dalla Torre; Jon I. Mujika; Elena Formoso; Eduard Matito; Maria J. Ramos; Xabier Lopez. "Tuning the affinity of catechols and salicylic acids towards Al(iii): characterization of Al–chelator interactions". Dalton Transactions 47 29 (2018): 9592-9607. https://doi.org/10.1039%2Fc8dt01341a.
    10.1039/c8dt01341a
  59. Biernacki, K.; Sousa, S. F.; Gales, L.; Ramos, M. J.; Magalhaes, A. L.. "Transport Properties of Light Gases in Nanochannels of L-Leu-L-Ser Dipeptide Crystals: A Comparative Study by Molecular Dynamics Simulations". Chemistryselect 3 20 (2018): 5517-5525. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000433494600004&KeyUID=WOS:000433494600004.
    10.1002/slct.201800559
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. Gonzalo A. Jaña; Fernanda Mendoza; Manuel I. Osorio; Joel B. Alderete; Pedro A. Fernandes; Maria J. Ramos; Verónica A. Jiménez. "A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans". Organic & Biomolecular Chemistry 16 14 (2018): 2438-2447. https://doi.org/10.1039%2Fc8ob00284c.
    10.1039/c8ob00284c
  67. Corley, MFV; Ferreira, S; Grundy, D; Nunes, J; Pires, P; Rosete, J; Goncalves, AR; Mata, V. "New and interesting Portuguese Lepidoptera records from 2017 (Insecta: Lepidoptera)". SHILAP-REVISTA DE LEPIDOPTEROLOGIA (2018):
  68. 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
  69. Paiva, P.; Costa, I. P. D.; Ferreira, C. E.; Ferreira, P.; Pereira, A. T.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Studies on neuraminidase inhibition". International Journal of Quantum Chemistry 118 9 (2018): 13-13. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000428413300014&KeyUID=WOS:000428413300014.
    10.1002/qua.25592
  70. 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
  71. 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
  72. Araujo, MP; Nunes, M; Rocha, IM; Pereira, MFR; Freire, C. "Co3O4 Nanoparticles Anchored on Selectively Oxidized Graphene Flakes as Bifunctional Electrocatalysts for Oxygen Reactions". CHEMISTRYSELECT (2018):
    10.1002/slct.201802108
  73. Simoes, Ines C. M.; Costa, Ines P. D.; Coimbra, Joao T. S.; Ramos, Maria J.; Fernandes, Pedro A.. "New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces". Journal of Chemical Information and Modeling 57 1 (2017): 60-72. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000392687400008&KeyUID=WOS:000392687400008.
    10.1021/acs.jcim.6b00378
  74. Barra, Pabla A.; Ribeiro, Antonio J. M.; Ramos, Maria J.; Jimenez, Veronica A.; Alderete, Joel B.; Fernandes, Pedro A.. "Binding free energy calculations on E-selectin complexes with sLe(x) oligosaccharide analogs". Chemical Biology & Drug Design 89 1 (2017): 114-123. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000390354100010&KeyUID=WOS:000390354100010.
    10.1111/cbdd.12837
  75. Fernandes, H S; Silva Teixeira, C S; Fernandes, P A; Ramos, M J; Cerqueira, N M F S A. "Amino acid deprivation using enzymes as a targeted therapy for cancer and viral infections.". Expert opinion on therapeutic patents 27 3 (2017): 283-297. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:27813440&KeyUID=MEDLINE:27813440.
    10.1080/13543776.2017.1254194
  76. Medina, Fabiola E.; Neves, Rui P. P.; Ramos, Maria J.; Fernandes, Pedro A.. "A QM/MM study of the reaction mechanism of human beta-ketoacyl reductase". Physical Chemistry Chemical Physics 19 1 (2017): 347-355. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000391725300037&KeyUID=WOS:000391725300037.
    10.1039/c6cp07014k
  77. Cerqueira, N. M. F. S. A.; Moorthy, H.; Fernandes, P. A.; Ramos, M. J.. "The mechanism of the Ser-(cis)Ser-Lys catalytic triad of peptide amidases". Physical Chemistry Chemical Physics 19 19 (2017): 12343-12354. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000401640600062&KeyUID=WOS:000401640600062.
    10.1039/c7cp00277g
  78. Coimbra, Joao T. S.; Fernandes, Pedro A.; Ramos, Maria J.. "Revisiting Partition in Hydrated Bilayer Systems". Journal of Chemical Theory and Computation 13 5 (2017): 2290-2299. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000401221300036&KeyUID=WOS:000401221300036.
    10.1021/acs.jctc.6b01258
  79. Hu, Zhang; Sim, Ying; Kon, Oi Lian; Ng, Wai Har; Ribeiro, Antonio J. M.; Ramos, Maria J.; Fernandes, Pedro A.; et al. "Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy". Bioconjugate Chemistry 28 2 (2017): 590-599. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000394481700036&KeyUID=WOS:000394481700036.
    10.1021/acs.bioconjchem.6b00682
  80. 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
  81. 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.
  82. Merski, M.; Moreira, C.; Abreu, R. M. V.; Ramos, M. J.; Fernandes, P. A.; Martins, L. M.; Pereira, P. J. B.; Macedo-Ribeiro, S.. "Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2". Cell Death & Disease 8 (2017): 10-10. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000414022900040&KeyUID=WOS:000414022900040.
    10.1038/cddis.2017.487
  83. Neves, Rui P. P.; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. "Mechanistic insights on the reduction of glutathione disulfide by protein disulfide isomerase". Proceedings of the National Academy of Sciences of the United States of America 114 24 (2017): E4724-E4733. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000403179300004&KeyUID=WOS:000403179300004.
    10.1073/pnas.1618985114
  84. Pereira, A. T.; Ribeiro, A. J. M.; Fernandes, P. A.; Ramos, M. J.. "Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases". International Journal of Quantum Chemistry 117 18 (2017): 12-12. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000406687800002&KeyUID=WOS:000406687800002.
    10.1002/qua.25409
  85. Sousa, Sergio Filipe; Ribeiro, Antnio J. M.; Neves, Rui P. P.; Bras, Natercia F.; Cerqueira, Nuno M. F. S. A.; Fernandes, Pedro A.; Ramos, Maria Joao. "Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms". Wiley Interdisciplinary Reviews-Computational Molecular Science 7 2 (2017): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000399013100004&KeyUID=WOS:000399013100004.
    10.1002/wcms.1281
  86. Ribeiro, Rui P.; Coimbra, Joao T. S.; Ramos, Maria J.; Fernandes, Pedro A.. "Diffusion of the small, very polar, drug piracetam through a lipid bilayer: an MD simulation study". Theoretical Chemistry Accounts 136 4 (2017): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000404246000001&KeyUID=WOS:000404246000001.
    10.1007/s00214-017-2073-3
  87. 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
  88. Nunes, M; Moura, C; Hillman, AR; Freire, C. "Novel hybrid based on a poly[Ni(salen)] film and WO3 nanoparticles with electrochromic properties". ELECTROCHIMICA ACTA (2017):
    10.1016/j.electacta.2017.04.010
  89. Proenca, C; Freitas, M; Ribeiro, D; Oliveira, EFT; Sousa, JLC; Tome, SM; Ramos, MJ; et al. "alpha-Glucosidase inhibition by flavonoids: an in vitro and in silico structure-activity relationship study". JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY (2017):
    10.1080/14756366.2017.1368503
  90. Ferreira, P; Sousa, SF; Fernandes, PA; Ramos, MJ. "Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives". CHEMISTRY-A EUROPEAN JOURNAL (2017):
    10.1002/chem.201704057
  91. Fernandes, H. S.; Ramos, M. J.; Cerqueira, Nmfsa. "The Catalytic Mechanism of the Pyridoxal-5 '-phosphate-Dependent Enzyme, Histidine Decarboxylase: A Computational Study". Chemistry-a European Journal 23 38 (2017): 9162-9173. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000404854700024&KeyUID=WOS:000404854700024.
    10.1002/chem.201701375
  92. Santos-Martins, Diogo; Fernandes, Pedro Alexandrino; Ramos, Maria Joo. "Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas". Journal of Computer-Aided Molecular Design 30 11 (2016): 1079-1086. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000391459000013&KeyUID=WOS:000391459000013.
    10.1007/s10822-016-9951-y
  93. Neves, Rui P. P.; Fernandes, Pedro A.; Ramos, Maria J.. "Unveiling the Catalytic Mechanism of NADP(+)-Dependent Isocitrate Dehydrogenase with QM/MM Calculations". Acs Catalysis 6 1 (2016): 357-368. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000367706800039&KeyUID=WOS:000367706800039.
    10.1021/acscatal.5b01928
  94. Bras, Natercia F.; Ferreira, Pedro; Calixto, Ana R.; Jaspars, Marcel; Houssen, Wael; Naismith, James H.; Fernandes, Pedro A.; Ramos, Maria J.. "The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac". Chemistry-a European Journal 22 37 (2016): 13089-13097. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000383763200022&KeyUID=WOS:000383763200022.
    10.1002/chem.201601670
  95. Moreira, Catia; Ramos, Maria J.; Fernandes, Pedro Alexandrino. "Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations". Chemistry-a European Journal 22 27 (2016): 9218-9225. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000380271100028&KeyUID=WOS:000380271100028.
    10.1002/chem.201600305
  96. Oliveira, Eduardo F.; Cerqueira, Nuno M. F. S. A.; Ramos, Maria J.; Fernandes, Pedro A.. "QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase". Catalysis Science & Technology 6 19 (2016): 7172-7185. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000384876400018&KeyUID=WOS:000384876400018.
    10.1039/c6cy00356g
  97. Moorthy, N. S. Hari Narayana; Sousa, Sergio F.; Ramos, Maria J.; Fernandes, Pedro A.. "Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery". Journal of Enzyme Inhibition and Medicinal Chemistry 31 6 (2016): 1428-1442. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000385270300073&KeyUID=WOS:000385270300073.
    10.3109/14756366.2016.1144593
  98. Sousa, Rui P.; Fernandes, Pedro A.; Ramos, Maria J.; Bras, Natercia F.. "Insights into the reaction mechanism of 3-O-sulfotransferase through QM/MM calculations". Physical Chemistry Chemical Physics 18 16 (2016): 11488-11496. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000374786300091&KeyUID=WOS:000374786300091.
    10.1039/c5cp06224a
  99. Sousa, Sergio F.; Sousa, Joana F. M.; Barbosa, Ana C. C.; Ferreira, Cleide E.; Neves, Rui P. P.; Ribeiro, Antonio J. M.; Fernandes, Pedro A.; Ramos, Maria Joao. "Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)". Journal of Physical Chemistry a 120 27 (2016): 5300-5306. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000379988900079&KeyUID=WOS:000379988900079.
    10.1021/acs.jpca.6b01536
  100. Oliveira, Eduardo Filipe; Santos-Martins, Diogo; Ribeiro, Antonio Meireles; Bras, Natercia Fernandes; Cerqueira, Nuno Sousa; Sousa, Sergio Filipe; Ramos, Maria Joao; Fernandes, Pedro Alexandrino. "HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015)". Expert Opinion on Therapeutic Patents 26 11 (2016): 1257-1272. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000386784000004&KeyUID=WOS:000386784000004.
    10.1080/13543776.2016.1216977
  101. Moreira, Catia; Ramos, Maria J.; Fernandes, Pedro A.. "Glutamine Synthetase Drugability beyond Its Active Site: Exploring Oligomerization Interfaces and Pockets". Molecules 21 8 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000382334600067&KeyUID=WOS:000382334600067.
    10.3390/molecules21081028
  102. Cerqueira, Nuno M. F. S. A.; Oliveira, Eduardo F.; Gesto, Diana S.; Santos-Martins, Diogo; Moreira, Catia; Moorthy, Hari N.; Ramos, Maria J.; Fernandes, P. A.. "Cholesterol Biosynthesis: A Mechanistic Overview". Biochemistry 55 39 (2016): 5483-5506. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000384842100001&KeyUID=WOS:000384842100001.
    10.1021/acs.biochem.6b00342
  103. Moorthy, N. S. Hari Narayana; Sousa, Sergio F.; Ramos, Maria J.; Fernandes, Pedro A.. "Binding mode of conformations and structure-based pharmacophore development for farnesyltransferase inhibitors". Medicinal Chemistry Research 25 7 (2016): 1340-1357. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000378573400006&KeyUID=WOS:000378573400006.
    10.1007/s00044-016-1578-y
  104. Gama, J; Dias, G; Couceiro, M; Passos, P; Davids, K; Ribeiro, J. "An ecological dynamics rationale to explain home advantage in professional football". INTERNATIONAL JOURNAL OF MODERN PHYSICS C (2016):
    10.1142/s0129183116501023
  105. Nunes, M; Fernandes, DM; Rocha, IM; Pereira, MFR; Mbomekalle, IM; de Oliveira, P; Freire, C. "Phosphomolybdate@Carbon-Based Nanocomposites as Electrocatalysts for Oxygen Reduction Reaction". CHEMISTRYSELECT (2016):
    10.1002/slct.201601370
  106. Fernandes, DM; Nunes, M; Araujo, MP. "Carbon Nanomaterials-based modified electrodes for Electrocatalysis". BOLETIN DEL GRUPO ESPANOL DEL CARBON (2016):
  107. Llinas, Paola; Chenon, Melanie; Quyen Nguyen, T.; Moreira, Catia; de Regibus, Annelie; Coquard, Aline; Ramos, Maria J.; et al. "Structure of a truncated form of leucine zipper II of JIP3 reveals an unexpected antiparallel coiled-coil arrangement". Acta Crystallographica Section F-Structural Biology Communications 72 (2016): 198-206. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000371619200006&KeyUID=WOS:000371619200006.
    10.1107/s2053230x16001576
  108. 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
  109. 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
  110. Shi, Y. X.; Liang, R. Z.; Martin, K. A.; Weston, N.; Gonzalez-Calera, S.; Ganguly, R.; Li, Y. X.; et al. "Synthesis and Hydrolytic Studies on the Air-Stable (4-CN-PhO)(E)P(mu-(NBu)-Bu-t) (2) (E = O, S, and Se) Cyclodiphosphazanes". Inorganic Chemistry 54 13 (2015): 6423-6432. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000357705800044&KeyUID=WOS:000357705800044.
    10.1021/acs.inorgchem.5b00735
  111. 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
  112. Cerqueira, Nmfsa; Gesto, D.; Oliveira, E. F.; Santos-Martins, D.; Bras, N. F.; Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Receptor-based virtual screening protocol for drug discovery". Archives of Biochemistry and Biophysics 582 (2015): 56-67. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000360781200007&KeyUID=WOS:000360781200007.
    10.1016/j.abb.2015.05.011
  113. Pinto, G. P.; Ribeiro, A. J. M.; Ramos, M. J.; Fernandes, P. A.; Toscano, M.; Russo, N.. "New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models". Archives of Biochemistry and Biophysics 582 (2015): 107-115. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000360781200012&KeyUID=WOS:000360781200012.
    10.1016/j.abb.2015.03.002
  114. 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
  115. Moorthy, Nshn; Cerqueira, Nmfsa; Ramos, M. J.; Fernandes, P. A.. "Ligand based analysis on HMG-CoA reductase inhibitors". Chemometrics and Intelligent Laboratory Systems 140 (2015): 102-116. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000349062500011&KeyUID=WOS:000349062500011.
    10.1016/j.chemolab.2014.11.009
  116. Ribeiro, A. J. M.; Yang, L. F.; Ramos, M. J.; Fernandes, P. A.; Liang, Z. X.; Hirao, H.. "Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase". Acs Catalysis 5 6 (2015): 3740-3751. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000355964300062&KeyUID=WOS:000355964300062.
    10.1021/acscatal.5b00528
  117. Cerqueira, Nmfsa; Coelho, C.; Bras, N. F.; Fernandes, P. A.; Garattini, E.; Terao, M.; Romao, M. J.; Ramos, M. J.. "Insights into the structural determinants of substrate specificity and activity in mouse aldehyde oxidases". Journal of Biological Inorganic Chemistry 20 2 (2015): 209-217. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000350236100004&KeyUID=WOS:000350236100004.
    10.1007/s00775-014-1198-2
  118. Ribeiro, A. J. M.; Santos-Martins, D.; Russo, N.; Rarnos, M. J.; Fernandes, P. A.. "Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease". Acs Catalysis 5 9 (2015): 5617-5626. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000361089700073&KeyUID=WOS:000361089700073.
    10.1021/acscatal.5b00759
  119. Pinto, G. P.; Bras, N. F.; Perez, M. A. S.; Fernandes, P. A.; Russo, N.; Ramos, M. J.; Toscano, M.. "Establishing the Catalytic Mechanism of Human Pancreatic alpha-Amylase with QM/MM Methods". Journal of Chemical Theory and Computation 11 6 (2015): 2508-2516. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000356201700012&KeyUID=WOS:000356201700012.
    10.1021/acs.jctc.5b00222
  120. Moreira, I. S.; Martins, J. M.; Coimbra, J. T. S.; Ramos, M. J.; Fernandes, P. A.. "A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy". Physical Chemistry Chemical Physics 17 4 (2015): 2378-2387. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000346906700012&KeyUID=WOS:000346906700012.
    10.1039/c4cp04688a
  121. Moorthy, NSHN; Bras, NF; Ramos, MJ; Fernandes, PA. "Binding mode prediction and identification of new lead compounds from natural products as renin and angiotensin converting enzyme inhibitors". RSC ADVANCES (2014): https://www.authenticus.pt/P-009-DFG.
    10.1039/c4ra00856a
  122. Bidarian Moniri, A; Ramos, MJ; Ejnell, H. "Autoinflation for treatment of persistent otitis media with effusion in children: A cross-over study with a 12-month follow-up". INTERNATIONAL JOURNAL OF PEDIATRIC OTORHINOLARYNGOLOGY (2014):
    10.1016/j.ijporl.2014.05.015
  123. 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
  124. Silva, A. M. N.; Sousa, P. R. H.; Coimbra, J. T. S.; Bras, N. F.; Vitorino, R.; Fernandes, P. A.; Ramos, M. J.; Rangel, M.; Domingues, P.. "The glycation site specificity of human serum transferrin is a determinant for transferrin's functional impairment under elevated glycaemic conditions". Biochemical Journal 461 (2014): 33-42. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000337770800003&KeyUID=WOS:000337770800003.
    10.1042/bj20140133
  125. Fernandes, A.; Ivanova, G.; Bras, N. F.; Mateus, N.; Ramos, M. J.; Rangel, M.; de Freitas, V.. "Structural characterization of inclusion complexes between cyanidin-3-0-glucoside and beta-cyclodextrin". Carbohydrate Polymers 102 (2014): 269-277. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000331779600035&KeyUID=WOS:000331779600035.
    10.1016/j.carbpol.2013.11.037
  126. Aranda, J.; Cerqueira, Nmfsa; Fernandes, P. A.; Roca, M.; Tunon, I.; Ramos, M. J.. "The Catalytic Mechanism of Carboxylesterases: A Computational Study". Biochemistry 53 36 (2014): 5820-5829. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000341801000012&KeyUID=WOS:000341801000012.
    10.1021/bi500934j
  127. Coimbra, J. T. S.; Moniz, T.; Bras, N. F.; Iyanova, G.; Fernandes, P. A.; Ramos, M. J.; Rangel, M.. "Relevant Interactions of Antimicrobial Iron Chelators and Membrane Models Revealed by Nuclear Magnetic Resonance and Molecular Dynamics Simulations". Journal of Physical Chemistry B 118 50 (2014): 14590-14601. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000346759400004&KeyUID=WOS:000346759400004.
    10.1021/jp509491p
  128. Marcial, B. L.; Sousa, S. F.; Dos Santos, H. F.; Ramos, M. J.. "Structural and dynamics analysis of matrix metalloproteinases MMP-2 complexed with chemically modified tetracyclines (CMTs)". Journal of Biomolecular Structure & Dynamics 32 12 (2014): 1907-1918. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340447600002&KeyUID=WOS:000340447600002.
    10.1080/07391102.2013.842186
  129. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "QM/MM Study and MD Simulations on the Hypertension Regulator Angiotensin-Converting Enzyme". Acs Catalysis 4 8 (2014): 2587-2597. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000339983800021&KeyUID=WOS:000339983800021.
    10.1021/cs500093h
  130. Calixto, A. R.; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Reaction Mechanism of Human Renin Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations". Acs Catalysis 4 11 (2014): 3869-3876. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344639300008&KeyUID=WOS:000344639300008.
    10.1021/cs500497f
  131. Martins, S. A.; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field". Journal of Chemical Theory and Computation 10 8 (2014): 3570-3577. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340351200067&KeyUID=WOS:000340351200067.
    10.1021/ct500346y
  132. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Predictive QSAR models development and validation for human ether-a-go-go related gene (hERG) blockers using newer tools". Journal of Enzyme Inhibition and Medicinal Chemistry 29 3 (2014): 317-324. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000336311600003&KeyUID=WOS:000336311600003.
    10.3109/14756366.2013.779264
  133. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Molecular dynamics studies on both bound and unbound renin protease". Journal of Biomolecular Structure & Dynamics 32 3 (2014): 351-363. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000329823600002&KeyUID=WOS:000329823600002.
    10.1080/07391102.2013.768553
  134. Ngo, H. P. T.; Cerqueira, Nmfsa; Kim, J. K.; Hong, M. K.; Fernandes, P. A.; Ramos, M. J.; Kang, L. W.. "PLP undergoes conformational changes during the course of an enzymatic reaction". Acta Crystallographica Section D-Biological Crystallography 70 (2014): 596-606. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000331554500038&KeyUID=WOS:000331554500038.
    10.1107/s1399004713031283
  135. Coimbra, J. T. S.; Neves, R. P. P.; Passos, O.; Jarukanont, D.; Fernandes, P. A.; Patel, S.; Garcia, M. E.; Ramos, M. J.. "Influence of the environment on protein bond energies". Chemical Physics Letters 615 (2014): 75-82. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344747400014&KeyUID=WOS:000344747400014.
    10.1016/j.cplett.2014.09.066
  136. Dourado, Dfar; Fernandes, P. A.; Mannervik, B.; Ramos, M. J.. "Isomerization of Delta(5)-Androstene-3,17-dione into Delta(4)-Androstene-3, 17-dione Catalyzed by Human Glutathione Transferase A3-3: A Computational Study Identifies a Dual Role for Glutathione". Journal of Physical Chemistry A 118 31 (2014): 5790-5800. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340222500008&KeyUID=WOS:000340222500008.
    10.1021/jp410810q
  137. Moorthy, Nshn; Pratheepa, V.; Ramos, M. J.; Vasconcelos, V.; Fernandes, P. A.. "Fused Aryl-Phenazines: Scaffold for the Development of Bioactive Molecules". Current Drug Targets 15 7 (2014): 681-688. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000337168100003&KeyUID=WOS:000337168100003.
    10.2174/1389450115666140205152007
  138. Bras, N. F.; Cerqueira, Nmfsa; Ramos, M. J.; Fernandes, P. A.. "Glycosidase inhibitors: a patent review (2008-2013)". Expert Opinion on Therapeutic Patents 24 8 (2014): 857-874. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340430700003&KeyUID=WOS:000340430700003.
    10.1517/13543776.2014.916280
  139. Hong, M. K.; Ribeiro, A. J. M.; Kim, J. K.; Ngo, H. P. T.; Kim, J.; Lee, C. H.; Ahn, Y. J.; et al. "Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli". Acta Crystallographica Section D-Biological Crystallography 70 (2014): 1297-1310. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000335952500012&KeyUID=WOS:000335952500012.
    10.1107/s1399004714002570
  140. Sousa, S. F.; Cerqueira, Nmfsa; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Enzymatic "Tricks": Carboxylate Shift and Sulfur Shift". International Journal of Quantum Chemistry 114 19 (2014): 1253-1256. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000341718400003&KeyUID=WOS:000341718400003.
    10.1002/qua.24689
  141. Gesto, D. S.; Cerqueira, Nmfsa; Ramos, M. J.; Fernandes, P. A.. "Discovery of new druggable sites in the anti-cholesterol target HMG-CoA reductase by computational alanine scanning mutagenesis". Journal of Molecular Modeling 20 4 (2014): 13-13. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000334934900044&KeyUID=WOS:000334934900044.
    10.1007/s00894-014-2178-8
  142. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Discovery of New Sites for Drug Binding to the Hypertension-Related Renin-Angiotensinogen Complex". Chemical Biology & Drug Design 83 4 (2014): 427-439. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000332886400006&KeyUID=WOS:000332886400006.
    10.1111/cbdd.12258
  143. Ribeiro, J. V.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "chem-path-tracker: An Automated Tool to Analyze Chemical Motifs in Molecular Structures". Chemical Biology & Drug Design 84 1 (2014): 44-53. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000337665900004&KeyUID=WOS:000337665900004.
    10.1111/cbdd.12349
  144. Moorthy, Nshn; Martins, S. A.; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Classification study of solvation free energies of organic molecules using machine learning techniques". Rsc Advances 4 106 (2014): 61624-61630. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000345656600051&KeyUID=WOS:000345656600051.
    10.1039/c4ra07961b
  145. Araujo, A. R.; Ribeiro, A. J. M.; Fernandes, P. A.; Ramos, M. J.. "Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations". Journal of Chemical Theory and Computation 10 12 (2014): 5458-5466. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000346324000026&KeyUID=WOS:000346324000026.
    10.1021/ct500570g
  146. Jarukanont, D.; Coimbra, J. T. S.; Bauerhenne, B.; Fernandes, P. A.; Patel, S.; Ramos, M. J.; Garcia, M. E.. "Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase". Physical Chemistry Chemical Physics 16 39 (2014): 21768-21777. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000343072900083&KeyUID=WOS:000343072900083.
    10.1039/c4cp02289k
  147. Santos-Martins, D.; Forli, S.; Ramos, M. J.; Olson, A. J.. "AutoDock4(Zn): An Improved Auto Dock Force Field for Small-Molecule Docking to Zinc Metalloproteins". Journal of Chemical Information and Modeling 54 8 (2014): 2371-2379. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340861900018&KeyUID=WOS:000340861900018.
    10.1021/ci500209e
  148. Neves, R. P. P.; Fernandes, P. A.; Varandas, A. J. C.; Ramos, M. J.. "Benchmarking of Density Functionals for the Accurate Description of Thiol-Disulfide Exchange". Journal of Chemical Theory and Computation 10 11 (2014): 4842-4856. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344905300010&KeyUID=WOS:000344905300010.
    10.1021/ct500840f
  149. Bras, N. F.; Ribeiro, A. J. M.; Oliveira, M.; Paixao, N. M.; Tamames, J. A.; Fernandes, P. A.; Ramos, M. J.. "Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns". Journal of Molecular Modeling 20 6 (2014): 14-14. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000338632200028&KeyUID=WOS:000338632200028.
    10.1007/s00894-014-2271-z
  150. Moorthy, NSHN; Sousa, SF; Ramos, MJ; Fernandes, PA. "Farnesyltransferase Inhibitors: A Comprehensive Review Based on Quantitative Structural Analysis". CURRENT MEDICINAL CHEMISTRY (2013): https://www.authenticus.pt/P-006-JES.
    10.2174/09298673113206660262
  151. Bidarian Moniri, A; Ramos, MJ; Goncalves, I; Ejnell, H. "A new device for treatment of persistent otitis media with effusion". International Journal of Pediatric Otorhinolaryngology (2013):
    10.1016/j.ijporl.2013.10.009
  152. 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.
  153. Oliveira, B. L.; Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.; Santos, I.; Correia, J. D. G.. "Theoretical studies on the binding of rhenium(I) complexes to inducible nitric oxide synthase". Journal of Molecular Graphics & Modelling 45 (2013): 13-25. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000326849200002&KeyUID=WOS:000326849200002.
    10.1016/j.jmgm.2013.07.007
  154. Moreira, I. S.; Martins, J. M.; Ramos, R. M.; Fernandes, P. A.; Ramos, M. J.. "Understanding the importance of the aromatic amino-acid residues as hot-spots". Biochimica Et Biophysica Acta-Proteins and Proteomics 1834 1 (2013): 404-414. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000314620400042&KeyUID=WOS:000314620400042.
    10.1016/j.bbapap.2012.07.005
  155. Cerqueira, Nmfsa; Fernandes, P. A.; Gonzalez, P. J.; Moura, J. J. G.; Ramos, M. J.. "The Sulfur Shift: An Activation Mechanism for Periplasmic Nitrate Reductase and Formate Dehydrogenase". Inorganic Chemistry 52 19 (2013): 10766-10772. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000326319800017&KeyUID=WOS:000326319800017.
    10.1021/ic3028034
  156. Teixeira, N.; Cruz, L.; Bras, N. F.; Mateus, N.; Ramos, M. J.; de Freitas, V.. "Structural Features of Copigmentation of Oenin with Different Polyphenol Copigments". Journal of Agricultural and Food Chemistry 61 28 (2013): 6942-6948. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000322103600022&KeyUID=WOS:000322103600022.
    10.1021/jf401174b
  157. Ornellas, F. R.; Ramos, M. J.. "Preface". Theoretical Chemistry Accounts 132 3 (2013): 5-5. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000318295200002&KeyUID=WOS:000318295200002.
    10.1007/s00214-012-1319-3
  158. Sousa, S. F.; Ribeiro, A. J. M.; Coimbra, J. T. S.; Neves, R. P. P.; Martins, S. A.; Moorthy, Nshn; Fernandes, P. A.; Ramos, M. J.. "Protein-Ligand Docking in the New Millennium - A Retrospective of 10 Years in the Field". Current Medicinal Chemistry 20 18 (2013): 2296-2314. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000318486200002&KeyUID=WOS:000318486200002.
    10.2174/0929867311320180002
  159. Carvalho, A. T. P.; Teixeira, A. F. S.; Ramos, M. J.. "Parameters for molecular dynamics simulations of iron-sulfur proteins". Journal of Computational Chemistry 34 18 (2013): 1540-1548. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000320177700003&KeyUID=WOS:000320177700003.
    10.1002/jcc.23287
  160. Silva, P. J.; Perez, M. A. S.; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Improving the study of proton transfers between amino acid side chains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls (vol 131, pg 1179, 2012)". Theoretical Chemistry Accounts 132 2 (2013): 1-1. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000318294700003&KeyUID=WOS:000318294700003.
    10.1007/s00214-012-1307-7
  161. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Human Ether-a-Go-Go-Related Gene Channel Blockers and its Structural Analysis for Drug Design". Current Drug Targets 14 1 (2013): 102-113. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000316871200011&KeyUID=WOS:000316871200011.
  162. Gesto, D. S.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Unraveling the Enigmatic Mechanism of L-Asparaginase II with QM/QM Calculations". Journal of the American Chemical Society 135 19 (2013): 7146-7158. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000319250200017&KeyUID=WOS:000319250200017.
    10.1021/ja310165u
  163. Moorthy, Nshn; Cerqueira, Nmfsa; Ramos, M. J.; Fernandes, P. A.. "Combined ligand and structure based binding mode analysis of oxidosqualene cyclase inhibitors". Rsc Advances 3 45 (2013): 23409-23422. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000326395800097&KeyUID=WOS:000326395800097.
    10.1039/c3ra43670e
  164. 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://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000322703400003&KeyUID=WOS:000322703400003.
    10.1002/jcc.23349
  165. Moreira, I. S.; Martins, J. M.; Ramos, R. M.; Fernandes, P. A.; Ramos, M. J.; Moreira, I.S.; Ramos, R.M.; et al. "Are Hot-Spots Occluded from Water?". Biophysical Journal 104 2 (2013): 505A-505A. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000316074305069&KeyUID=WOS:000316074305069.
    10.1080/07391102.2012.758598
  166. Ribeiro, A. J. M.; Ramos, M. J.; Fernandes, P. A.; Russo, N.. "A DFT study of the applicability of the charge balance model in two-metal enzymes: The case of cAMP-dependent protein kinase". Chemical Physics Letters 571 (2013): 66-70. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000319109900011&KeyUID=WOS:000319109900011.
    10.1016/j.cplett.2013.03.085
  167. 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
  168. 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
  169. 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
  170. 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
  171. 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
  172. 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
  173. 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
  174. 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
  175. Oliveira, J.; Da Silva, M.A.; Parola, A.J.; Mateus, N.; Brás, N.F.; Ramos, M.J.; De Freitas, V.. "Structural characterization of a A-type linked trimeric anthocyanin derived pigment occurring in a young Port wine". Food Chemistry 141 3 (2013): 1987-1996. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879047061&partnerID=MN8TOARS.
    10.1016/j.foodchem.2013.04.091
  176. 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
  177. Moorthy, Nshn; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "In silico Based Structural Analysis of Some Piperidine Analogs as Farnesyltransferase Inhibitors". Medicinal Chemistry 8 5 (2012): 853-864. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000309650400011&KeyUID=WOS:000309650400011.
    10.2174/157340612802084171
  178. Moorthy, Nshn; Bras, N. F.; Ramos, M. J.; Fernandes, P. A.. "Virtual screening and QSAR study of some pyrrolidine derivatives as alpha-mannosidase inhibitors for binding feature analysis". Bioorganic & Medicinal Chemistry 20 24 (2012): 6945-6959. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000311421300006&KeyUID=WOS:000311421300006.
    10.1016/j.bmc.2012.10.011
  179. De Rienzo, F.; Barbosa, A. J. M.; Perez, M. A. S.; Fernandes, P. A.; Ramos, M. J.; Menziani, M. C.. "The extracellular subunit interface of the 5-HT3 receptors: a computational alanine scanning mutagenesis study". Journal of Biomolecular Structure & Dynamics 30 3 (2012): 280-298. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000306119000004&KeyUID=WOS:000306119000004.
    10.1080/07391102.2012.680029
  180. Bras, N. F.; Ramos, M. J.; Fernandes, P. A.. "The catalytic mechanism of mouse renin studied with QM/MM calculations". Physical Chemistry Chemical Physics 14 36 (2012): 12605-12613. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000307900800020&KeyUID=WOS:000307900800020.
    10.1039/c2cp41422h
  181. Moorthy, Nshn; Cerqueira, N. S.; Ramos, M. J.; Fernandes, P. A.. "QSAR analysis of 2-benzoxazolyl hydrazone derivatives for anticancer activity and its possible target prediction". Medicinal Chemistry Research 21 2 (2012): 133-144. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000298882100001&KeyUID=WOS:000298882100001.
    10.1007/s00044-010-9510-3
  182. Nave, F.; Bras, N. F.; Cruz, L.; Teixeira, N.; Mateus, N.; Ramos, M. J.; Di Meo, F.; et al. "Influence of a Flavan-3-ol Substituent on the Affinity of Anthocyanins (Pigments) toward Vinylcatechin Dimers and Proanthocyanidins (Copigments)". Journal of Physical Chemistry B 116 48 (2012): 14089-14099. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000311921700017&KeyUID=WOS:000311921700017.
    10.1021/jp307782y
  183. Ribeiro, J. V.; Cerqueira, Nmfsa; Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "CompASM: an Amber-VMD alanine scanning mutagenesis plug-in". Theoretical Chemistry Accounts 131 10 (2012): 7-7. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000309862600005&KeyUID=WOS:000309862600005.
    10.1007/s00214-012-1271-2
  184. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Computational enzymatic catalysis - clarifying enzymatic mechanisms with the help of computers". Physical Chemistry Chemical Physics 14 36 (2012): 12431-12441. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000307900800003&KeyUID=WOS:000307900800003.
    10.1039/c2cp41180f
  185. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Comparative Structural Analysis of a-Glucosidase Inhibitors on Difference Species: A Computational Study". Archiv Der Pharmazie 345 4 (2012): 265-274. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000302607300003&KeyUID=WOS:000302607300003.
    10.1002/ardp.201100047
  186. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Analysis of van der Waals surface area properties for human ether-a-go-go-related gene blocking activity: computational study on structurally diverse compounds". Sar and Qsar in Environmental Research 23 5-6 (2012): 521-536. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000306712600008&KeyUID=WOS:000306712600008.
    10.1080/1062936x.2012.666264
  187. Coelho, C.; Mahro, M.; Trincão, J.; Carvalho, A.T.P.; Ramos, M.J.; Terao, M.; Garattini, E.; Leimkühler, S.; Romão, M.J.. "The first mammalian aldehyde oxidase crystal structure: Insights into substrate specificity". Journal of Biological Chemistry 287 48 (2012): 40690-40702. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870012251&partnerID=MN8TOARS.
    10.1074/jbc.m112.390419
  188. Marcial, B.L.; Sousa, S.F.; Barbosa, I.L.; Dos Santos, H.F.; Ramos, M.J.. "Chemically modified tetracyclines as inhibitors of MMP-2 matrix metalloproteinase: A molecular and structural study". Journal of Physical Chemistry B 116 46 (2012): 13644-13654. http://www.scopus.com/inward/record.url?eid=2-s2.0-84869994239&partnerID=MN8TOARS.
    10.1021/jp3079748
  189. 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
  190. 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
  191. 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
  192. 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
  193. 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
  194. 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
  195. Silva, P.J.; Ramos, M.J.. "Computational characterization of the substrate-binding mode in coproporphyrinogen III oxidase". Journal of Physical Chemistry B 115 8 (2011): 1903-1910. http://www.scopus.com/inward/record.url?eid=2-s2.0-79951992419&partnerID=MN8TOARS.
    10.1021/jp110289d
  196. Cerqueira, Nmfsa; Ribeiro, J.; Fernandes, P. A.; Ramos, M. J.. "vsLab-An Implementation for Virtual High-Throughput Screening Using AutoDock and VMD". International Journal of Quantum Chemistry 111 6 (2011): 1208-1212. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000288096500009&KeyUID=WOS:000288096500009.
    10.1002/qua.22738
  197. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "The Catalytic Mechanism of RNA Polymerase II". Journal of Chemical Theory and Computation 7 4 (2011): 1177-1188. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000289315700039&KeyUID=WOS:000289315700039.
    10.1021/ct100579w
  198. Passos, O.; Fernandes, P. A.; Ramos, M. J.. "Theoretical insights into the catalytic mechanism of beta-hexosaminidase". Theoretical Chemistry Accounts 129 1 (2011): 119-129. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000289484000012&KeyUID=WOS:000289484000012.
    10.1007/s00214-011-0904-1
  199. Silva, P. J.; Ramos, M. J.. "Successes and failures of DFT functionals in acid/base and redox reactions of organic and biochemical interest". Computational and Theoretical Chemistry 966 1-3 (2011): 120-126. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000291325100018&KeyUID=WOS:000291325100018.
    10.1016/j.comptc.2011.02.022
  200. Neves, A. R.; Fernandes, P. A.; Ramos, M. J.. "The Accuracy of Density Functional Theory in the Description of Cation-pi and pi-Hydrogen Bond Interactions". Journal of Chemical Theory and Computation 7 7 (2011): 2059-2067. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000292617900007&KeyUID=WOS:000292617900007.
    10.1021/ct2001667
  201. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Structural analysis of alpha-glucosidase inhibitors by validated QSAR models using topological and hydrophobicity based descriptors". Chemometrics and Intelligent Laboratory Systems 109 2 (2011): 101-112. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000297392800001&KeyUID=WOS:000297392800001.
    10.1016/j.chemolab.2011.02.010
  202. Moorthy, Nshn; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors". Journal of Enzyme Inhibition and Medicinal Chemistry 26 6 (2011): 777-791. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000297057900003&KeyUID=WOS:000297057900003.
    10.3109/14756366.2011.552885
  203. Passos, O.; Fernandes, P. A.; Ramos, M. J.. "QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human beta-HexosaminidaseA". Journal of Physical Chemistry B 115 49 (2011): 14751-14759. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000297608600046&KeyUID=WOS:000297608600046.
    10.1021/jp205826n
  204. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "QSAR Analysis of Isosteviol Derivatives as alpha-Glucosidase Inhibitors with Element Count and Other Descriptors". Letters in Drug Design & Discovery 8 1 (2011): 14-25. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000285781700003&KeyUID=WOS:000285781700003.
    10.2174/157018011793663859
  205. Tamames, J. A. C.; Ramos, M. J.. "Metals in proteins: cluster analysis studies". Journal of Molecular Modeling 17 3 (2011): 429-442. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000289531200003&KeyUID=WOS:000289531200003.
    10.1007/s00894-010-0733-5
  206. Oliveira, E. F.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Mechanism of Formation of the Internal Aldimine in Pyridoxal 5 '-Phosphate-Dependent Enzymes". Journal of the American Chemical Society 133 39 (2011): 15496-15505. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000295911500052&KeyUID=WOS:000295911500052.
    10.1021/ja204229m
  207. Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "hERG binding feature analysis of structurally diverse compounds by QSAR and fragmental analysis". Rsc Advances 1 6 (2011): 1126-1136. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000295920900030&KeyUID=WOS:000295920900030.
    10.1039/c1ra00131k
  208. Bras, N. F.; Cruz, L.; Fernandes, P. A.; De Freitas, V.; Ramos, M. J.. "Conformational Study of Two Diasteroisomers of Vinylcatechin Dimers in a Methanol Solution". International Journal of Quantum Chemistry 111 7-8 (2011): 1498-1510. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000288873300029&KeyUID=WOS:000288873300029.
    10.1002/qua.22631
  209. Sousa, S. F.; Tamames, B.; Fernandes, P. A.; Ramos, M. J.. "Detailed Atomistic Analysis of the HIV-1 Protease Interface". Journal of Physical Chemistry B 115 21 (2011): 7045-7057. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000290914600027&KeyUID=WOS:000290914600027.
    10.1021/jp200075s
  210. Silva, P. J.; Ramos, M. J.. "Computational Insights Into the Photochemical Step of the Reaction Catalyzed by Protochlorophylide Oxidoreductase". International Journal of Quantum Chemistry 111 7-8 (2011): 1472-1479. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000288873300026&KeyUID=WOS:000288873300026.
    10.1002/qua.22671
  211. Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Computational Mechanistic Studies Addressed to the Transimination Reaction Present in All Pyridoxal 5 '-Phosphate-Requiring Enzymes". Journal of Chemical Theory and Computation 7 5 (2011): 1356-1368. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000290293000014&KeyUID=WOS:000290293000014.
    10.1021/ct1002219
  212. Oliveira, J.; Petrov, V.; Parola, A. J.; Pina, F.; Azevedo, J.; Teixeira, N.; Bras, N. F.; et al. "Chemical Behavior of Methylpyranomalvidin-3-O-glucoside in Aqueous Solution Studied by NMR and UV-Visible Spectroscopy". Journal of Physical Chemistry B 115 6 (2011): 1538-1545. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000287066600024&KeyUID=WOS:000287066600024.
    10.1021/jp110593c
  213. Bras, N. F.; Perez, M. A. S.; Fernandes, P. A.; Silva, P. J.; Ramos, M. J.. "Accuracy of Density Functionals in the Prediction of Electronic Proton Affinities of Amino Acid Side Chains". Journal of Chemical Theory and Computation 7 12 (2011): 3898-3908. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000298118000006&KeyUID=WOS:000298118000006.
    10.1021/ct200309v
  214. 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.
  215. 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
  216. 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
  217. 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
  218. 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
  219. Hari Narayana Moorthy, N.S.; Ramos, M.J.; Fernandes, P.A.; Moorthy, Nshn; Ramos, M. J.; Fernandes, P. A.. "Topological, hydrophobicity, and other descriptors on a-glucosidase inhibition: A QSAR study on xanthone derivatives". Journal of Enzyme Inhibition and Medicinal Chemistry 26 6 (2011): 755-766. http://www.scopus.com/inward/record.url?eid=2-s2.0-81355149312&partnerID=MN8TOARS.
    10.3109/14756366.2010.549089
  220. 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
  221. 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
  222. 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
  223. Silva, P.J.; Schulz, C.; Jahn, D.; Jahn, M.; Ramos, M.J.. "A tale of two acids: When arginine is a more appropriate acid than H 3O+". Journal of Physical Chemistry B 114 27 (2010): 8994-9001. http://www.scopus.com/inward/record.url?eid=2-s2.0-77954470518&partnerID=MN8TOARS.
    10.1021/jp100961s
  224. Alberto, M.E.; Marino, T.; Ramos, M.J.; Russo, N.. "Atomistic details of the catalytic mechanism of Fe(III)-Zn(II) purple acid phosphatase". Journal of Chemical Theory and Computation 6 8 (2010): 2424-2433. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955583791&partnerID=MN8TOARS.
    10.1021/ct100187c
  225. 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
  226. 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
  227. Perez, M. A. S.; Fernandes, P. A.; Ramos, M. J.. "Understanding the Mechanism for Ribonucleotide Reductase Inactivation by 2 '-Deoxy-2 '-methylenecytidine-5 '-diphosphate". Journal of Chemical Theory and Computation 6 9 (2010): 2770-2781.
    10.1021/ct1002175
  228. Perez, M. A. S.; Fernandes, P. A.; Ramos, M. J.. "Substrate Recognition in HIV-1 Protease: A Computational Study". Journal of Physical Chemistry B 114 7 (2010): 2525-2532.
    10.1021/jp910958u
  229. Bras, N. F.; Goncalves, R.; Fernandes, P. A.; Mateus, N.; Ramos, M. J.; de Freitas, V.. "Understanding the Binding of Procyanidins to Pancreatic Elastase by Experimental and Computational Methods". Biochemistry 49 25 (2010): 5097-5108.
    10.1021/bi100410q
  230. Dourado, Dfar; Fernandes, P. A.; Ramos, M. J.. "Glutathione Transferase Classes Alpha, Pi, and Mu: GSH Activation Mechanism". Journal of Physical Chemistry B 114 40 (2010): 12972-12980.
    10.1021/jp1053875
  231. Barbosa, A. J. M.; De Rienzo, F.; Ramos, M. J.; Menziani, M. C.. "Computational analysis of ligand recognition sites of homo- and heteropentameric 5-HT3 receptors". European Journal of Medicinal Chemistry 45 11 (2010): 4746-4760. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000283911300007&KeyUID=WOS:000283911300007.
    10.1016/j.ejmech.2010.07.039
  232. Ramos, M. J.. "Computational enzymatic catalysis". Febs Journal 277 (2010): 25-25. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000278565100097&KeyUID=WOS:000278565100097.
    10.1021/ar7001045
  233. Ribeiro, A. J. M.; Ramos, M. J.; Fernandes, P. A.. "Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds". Journal of Chemical Theory and Computation 6 8 (2010): 2281-2292. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000280661600003&KeyUID=WOS:000280661600003.
    10.1021/ct900649e
  234. Cruz, L.; Bras, N. F.; Teixeira, N.; Mateus, N.; Ramos, M. J.; Dangles, O.; De Freitas, V.. "Vinylcatechin Dimers Are Much Better Copigments for Anthocyanins than Catechin Dimer Procyanidin B3". Journal of Agricultural and Food Chemistry 58 5 (2010): 3159-3166. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000275087600080&KeyUID=WOS:000275087600080.
    10.1021/jf9037419
  235. Sousa, S. F.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Virtual Screening in Drug Design and Development". Combinatorial Chemistry & High Throughput Screening 13 5 (2010): 442-453. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000277889700008&KeyUID=WOS:000277889700008.
    10.2174/138620710791293001
  236. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "QM/MM Studies on the beta-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions". Journal of Chemical Theory and Computation 6 2 (2010): 421-433. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000274838800008&KeyUID=WOS:000274838800008.
    10.1021/ct900530f
  237. Bras, N. F.; Goncalves, R.; Mateus, N.; Fernandes, P. A.; Ramos, M. J.; Do Freitas, V.. "Inhibition of Pancreatic Elastase by Polyphenolic Compounds". Journal of Agricultural and Food Chemistry 58 19 (2010): 10668-10676. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000282545000051&KeyUID=WOS:000282545000051.
    10.1021/jf1017934
  238. 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
  239. 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
  240. 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
  241. Silva, P.J.; Ramos, M.J.. "Computational studies on the reactivity of substituted 1,2-dihydro-1,2- azaborines". Journal of Organic Chemistry 74 16 (2009): 6120-6129. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349098090&partnerID=MN8TOARS.
    10.1021/jo900980d
  242. Pande, V.; Sousa, S.F.; Ramos, M.J.. "Direct covalent modification as a strategy to inhibit Nuclear Factor-Kappa B". Current Medicinal Chemistry 16 32 (2009): 4261-4273. http://www.scopus.com/inward/record.url?eid=2-s2.0-70450198853&partnerID=MN8TOARS.
    10.2174/092986709789578222
  243. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme". Bioorganic & Medicinal Chemistry 17 9 (2009): 3369-3378.
    10.1016/j.bmc.2009.03.055
  244. Sousa, S. F.; Carvalho, E. S.; Ferreira, D. M.; Tavares, I. S.; Fernandes, P. A.; Ramos, M. J.; Gomes, Janf. "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.
    10.1002/jcc.21304
  245. 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.
  246. 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
  247. 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.
  248. Sousa, S. F.; Lopes, A. B.; Fernandes, P. A.; Ramos, M. J.. "The Zinc proteome: a tale of stability and functionality". Dalton Transactions 38 (2009): 7946-7956.
    10.1039/b904404c
  249. Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Docking and molecular dynamics studies on the stereoselectivity in the enzymatic synthesis of carbohydrates". Theoretical Chemistry Accounts 122 5-6 (2009): 283-296.
    10.1007/s00214-009-0507-2
  250. Cerqueira, Nmfsa; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "MADAMM: A multistaged docking with an automated molecular modeling protocol". Proteins-Structure Function and Bioinformatics 74 1 (2009): 192-206. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000261757900017&KeyUID=WOS:000261757900017.
    10.1002/prot.22146
  251. Moura-Tamames, S.; Ramos, M. J.; Fernades, P. A.; Moura-Tamames, S. A.; Fernandes, P. A.. "Modelling beta-1,3-Exoglucanase- saccharide interactions: structure of the enzyme-substrate complex and enzyme binding to the cell wall". Febs Journal 276 8 (2009): 156-157. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000267069900446&KeyUID=WOS:000267069900446.
    10.1016/j.jmgm.2009.01.007
  252. Dourado, Dfar; Fernandes, P. A.; Ramos, M. J.. "Glutathione transferase A1-1: catalytic role of water". Theoretical Chemistry Accounts 124 1-2 (2009): 71-83. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000269219100007&KeyUID=WOS:000269219100007.
    10.1007/s00214-009-0582-4
  253. Tamames, B.; Fernandes, P. A.; Ramos, M. J.. "HIV-1 Protease: a computational mutagenesis analysis of the monomers interface". Febs Journal 276 (2009): 167-167. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000267069900481&KeyUID=WOS:000267069900481.
  254. Moura-Tamames, S. A.; Ramos, M. J.; Fernades, P. A.. "Exploring beta-1,3-Exoglucanase-polysaccharide interactions: molecular dynamics of the enzyme-substrate complex with or without a polysaccharide ligand bound in the flexible enzyme loops". Febs Journal 276 (2009): 156-156. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000267069900445&KeyUID=WOS:000267069900445.
  255. Carvalho, A. T. P.; Fernandes, P. A.; Swart, M.; van Stralen, J. N. P.; Bickelhaupt, F. M.; Ramos, M. J.. "Role of the Variable Active Site Residues in the Function of Thioredoxin Family Oxidoreductases". Journal of Computational Chemistry 30 5 (2009): 710-724. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000264225900003&KeyUID=WOS:000264225900003.
    10.1002/jcc.21086
  256. Silva, P.J.; Ramos, M.J.. "A comparative density-functional study of the reaction mechanism of the O2-dependent coproporphyrinogen III oxidase". Bioorganic and Medicinal Chemistry 16 6 (2008): 2726-2733. http://www.scopus.com/inward/record.url?eid=2-s2.0-40949117609&partnerID=MN8TOARS.
    10.1016/j.bmc.2008.01.008
  257. 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
  258. da Fonseca, R. R.; Johnson, W. E.; O'Brien, S. J.; Ramos, M. J.; Antunes, A.. "The adaptive evolution of the mammalian mitochondrial genome". Bmc Genomics 9 (2008):
    10.1186/1471-2164-9-119
  259. Martins, S.; Ramos, M. J.; Fernandes, P. A.. "The current status of the NNRTI family of antiretrovirals used in the HAART regime against HIV infection". Current Medicinal Chemistry 15 11 (2008): 1083-1095.
    10.2174/092986708784221467
  260. Dourado, Dfar; Fernandes, P. A.; Mannervik, B.; Ramos, M. J.. "Glutathione Transferase: New Model for Glutathione Activation". Chemistry-a European Journal 14 31 (2008): 9591-9598.
    10.1002/chem.200800946
  261. Pande, V.; Ramos, M. J.; Gago, F.. "The protein kinase inhibitor balanol: Structure-activity relationships and structure-based computational studies". Anti-Cancer Agents in Medicinal Chemistry 8 6 (2008): 638-645. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000258737800006&KeyUID=WOS:000258737800006.
  262. Russo, N.; Ramos, M. J.; Ugalde, J. M.; Eriksson, L. A.. "Special issue: Proceedings of the 3rd Theoretical Biophysics Symposium - Centraro, Italy, June 16-20, 2007 - Introduction". International Journal of Quantum Chemistry 108 11 (2008): 1-1. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000257642300001&KeyUID=WOS:000257642300001.
    10.1002/qua.21776
  263. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Farnesyltransferase inhibitors: A detailed chemical view on an elusive biological problem". Current Medicinal Chemistry 15 15 (2008): 1478-1492.
    10.2174/092986708784638825
  264. Preto, M. A. C.; Melo, A.; Rodrigues, L. M.; Maia, H. L. S.; Ramos, M. J.. "Structural Insight on the Activity of Type 1 Angiotensin II Peptide Antagonists Using MD Simulations". Journal of Physical Chemistry B 112 43 (2008): 13620-13628. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000260357700020&KeyUID=WOS:000260357700020.
    10.1021/jp802349w
  265. Dourado, Dfar; Fernandes, P. A.; Ramos, M. J.. "Mammalian cytosolic glutathione transferases". Current Protein & Peptide Science 9 4 (2008): 325-337. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000259487200002&KeyUID=WOS:000259487200002.
    10.2174/138920308785132677
  266. Carvalho, A. T. P.; Swart, M.; van Stralen, J. N. P.; Fernandes, P. A.; Ramos, M. J.; Bickelhaupt, F. M.. "Mechanism of thioredoxin-catalyzed disulfide reduction. Activation of the buried thiol and role of the variable active-site residues". Journal of Physical Chemistry B 112 8 (2008): 2511-2523. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000253355500025&KeyUID=WOS:000253355500025.
    10.1021/jp7104665
  267. Bras, N. F.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Carbohydrate-binding modules from family 11: Understanding the binding mode of polysaccharides". International Journal of Quantum Chemistry 108 11 (2008): 2030-2040. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000257642300016&KeyUID=WOS:000257642300016.
    10.1002/qua.21755
  268. Branco, R. J. F.; Seifert, A.; Budde, M.; Urlacher, V. B.; Ramos, M. J.; Pleiss, J.. "Anchoring effects in a wide binding pocket: The molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium". Proteins-Structure Function and Bioinformatics 73 3 (2008): 597-607. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000260515500006&KeyUID=WOS:000260515500006.
    10.1002/prot.22083
  269. Silva, P. J.; Ramos, M. J.. "Comparative density functional study of models for the reaction mechanism of uroporphyrinogen III synthase". Journal of Physical Chemistry B 112 10 (2008): 3144-3148.
    10.1021/jp076235f
  270. Marques, A. T.; Antunes, A.; Fernandes, P. A.; Ramos, M. J.. "Computational optimization of AG18051 inhibitor for amyloid-beta binding alcohol dehydrogenase enzyme". International Journal of Quantum Chemistry 108 11 (2008): 1982-1991.
    10.1002/qua.21716
  271. Ramos, M. J.; Fernandes, P. A.. "Computational enzymatic catalysis". Accounts of Chemical Research 41 6 (2008): 689-698.
    10.1021/ar7001045
  272. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Protein-protein recognition: a computational mutagenesis study of the MDM2-P53 complex". Theoretical Chemistry Accounts 120 4-6 (2008): 533-542.
    10.1007/s00214-008-0432-9
  273. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Molecular dynamics analysis of farnesyltransferase: A closer look into the amino acid behavior". International Journal of Quantum Chemistry 108 11 (2008): 1939-1950.
    10.1002/qua.21713
  274. Marques, A. T.; Fernandes, P. A.; Ramos, M. J.. "Molecular dynamics simulations of the amyloid-beta binding alcohol dehydrogenase (ABAD) enzyme". Bioorganic & Medicinal Chemistry 16 21 (2008): 9511-9518.
    10.1016/j.bmc.2008.09.043
  275. Bras, N. F.; Moura-Tamames, S. A.; Fernandes, P. A.; Ramos, M. J.. "Mechanistic Studies on the Formation of Glycosidase-Substrate and Glycosidase-Inhibitor Covalent Intermediates". Journal of Computational Chemistry 29 15 (2008): 2565-2574.
    10.1002/jcc.21013
  276. Viegas, A.; Bras, N. F.; Cerqueira, Nmfsa; Fernandes, P. A.; Prates, J. A. M.; Fontes, Cmga; Bruix, M.; et al. "Molecular determinants of ligand specificity in family 11 carbohydrate binding modules - an NMR, X-ray crystallography and computational chemistry approach". Febs Journal 275 10 (2008): 2524-2535.
    10.1111/j.1742-4658.2008.06401.x
  277. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Comparative assessment of theoretical methods for the determination of geometrical properties in biological zinc complexes". Journal of Physical Chemistry B 111 30 (2007): 9146-9152.
    10.1021/jp072538y
  278. Luo, S.-J.; Cai, Q.-X.; David, V.A.; Zhang, L.; Martelli, P.; Lim, N.T.-L.; Ferrand, N.; et al. "Erratum: Isolation and characterization of microsatellite markers in pangolins (Mammalia, Pholidota, Manis spp.) (Molecular Ecology Notes (2006) 7 (269-272))". Molecular Ecology Notes 7 3 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-34248209102&partnerID=MN8TOARS.
    10.1111/j.1471-8286.2007.01778.x
  279. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Vascular endothelial growth factor (VEGF) inhibition - A critical review". Anti-Cancer Agents in Medicinal Chemistry 7 2 (2007): 223-245. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000244009200005&KeyUID=WOS:000244009200005.
    10.2174/187152007780058687
  280. Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Ribonucleotide reductase: A critical enzyme for cancer chemotherapy and antiviral agents". Recent Patents on Anti-Cancer Drug Discovery 2 1 (2007): 11-29. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000246564300002&KeyUID=WOS:000246564300002.
    10.2174/157489207779561408
  281. Antunes, A.; Ramos, M. J.. "Gathering Computational Genomics and Proteomics to Unravel Adaptive Evolution". Evolutionary Bioinformatics 3 (2007): 207-209. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000206500600016&KeyUID=WOS:000206500600016.
  282. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Computational alanine scanning mutagenesis - An improved methodological approach". Journal of Computational Chemistry 28 3 (2007): 644-654.
    10.1002/jcc.20566
  283. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "General performance of density functionals". Journal of Physical Chemistry A 111 42 (2007): 10439-10452.
    10.1021/jp0734474
  284. Perez, M. A. S.; Fernandes, P. A.; Ramos, M. J.. "Drug design: New inhibitors for HIV-1 protease based on Nelfinavir as lead". Journal of Molecular Graphics & Modelling 26 3 (2007): 634-642.
    10.1016/j.jmgm.2007.03.009
  285. Santos, H. R. R.; Ujaque, G.; Ramos, M. J.; Gomes, Janf. "Effect of the tert-butiloxycarbonyl protecting group on the adsorption of protected amino-cyclopentene on the Si(100) surface". Physical Review B 75 12 (2007):
    10.1103/PhysRevB.75.125413
  286. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL-10". International Journal of Quantum Chemistry 107 2 (2007): 299-310.
    10.1002/qua.21193
  287. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism". Theoretical Chemistry Accounts 117 1 (2007): 171-181.
    10.1007/s00214-006-0170-9
  288. Tamames, B.; Sousa, S. F.; Tamames, J.; Fernandes, P. A.; Ramos, M. J.. "Analysis of zinc-ligand bond lengths in metalloproteins: Trends and patterns". Proteins-Structure Function and Bioinformatics 69 3 (2007): 466-475.
    10.1002/prot.21536
  289. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Backbone importance for protein-protein binding". Journal of Chemical Theory and Computation 3 3 (2007): 885-893.
    10.1021/ct6003824
  290. Antunes, A.; Pontius, J.; Ramos, M. J.; O'Brien, S. J.; Johnson, W. E.. "Mitochondrial introgressions into the nuclear genome of the domestic cat". Journal of Heredity 98 5 (2007): 414-420.
    10.1093/jhered/esm062
  291. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "Parameterization of AZT - A widely used nucleoside inhibitor of HIV-1 reverse transcriptase". International Journal of Quantum Chemistry 107 2 (2007): 292-298.
    10.1002/qua.21192
  292. Luo, S. J.; Cai, Q. X.; David, V. A.; Zhang, L.; Martelli, P.; Lim, N. T. L.; Ferrand, N.; et al. "Isolation and characterization of microsatellite markers in pangolins (Mammalia, Pholidota, Manis spp.)". Molecular Ecology Notes 7 2 (2007): 269-272.
    10.1111/j.1471-8286.2006.01577.x
  293. Santos, H. R. R.; Ramos, M. J.; Gomes, Janf. "Microscopic detail provided for the adsorption of protected amino-cyclopentene on Si(100)". Chemical Physics Letters 448 1-3 (2007): 111-114.
    10.1016/j.cplett.2007.09.064
  294. Osorio, D. S.; Antunes, A.; Ramos, M. J.. "Structural and functional implications of positive selection at the primate angiogenin gene". Bmc Evolutionary Biology 7 (2007):
    10.1186/1471-2148-7-167
  295. Silva, P. J.; Ramos, M. J.. "Reaction mechanism of the vitamin K-dependent glutamate carboxylase: A computational study". Journal of Physical Chemistry B 111 44 (2007): 12883-12887.
    10.1021/jp0738208
  296. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Hot spot occlusion from bulk water: A comprehensive study of the complex between the lysozyme HEL and the antibody FVD1.3". Journal of Physical Chemistry B 111 10 (2007): 2697-2706.
    10.1021/jp067096p
  297. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Hot spots-A review of the protein-protein interface determinant amino-acid residues". Proteins-Structure Function and Bioinformatics 68 4 (2007): 803-812.
    10.1002/prot.21396
  298. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "The excision mechanism in reverse transcriptase: Pyrophosphate leaving and fingers opening are uncoupled events with the analogues AZT and d4T". Journal of Physical Chemistry B 111 41 (2007): 12032-12039.
    10.1021/jp0746594
  299. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Theoretical studies on farnesyltransferase: Evidence for thioether product coordination to the active-site zinc sphere". Journal of Computational Chemistry 28 7 (2007): 1160-1168.
    10.1002/jcc.20577
  300. da Fonseca, R. R.; Antunes, A.; Melo, A.; Ramos, M. J.. "Structural divergence and adaptive evolution in mammalian cytochromes P4502C". Gene 387 1-2 (2007): 58-66.
    10.1016/j.gene.2006.08.017
  301. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "The carboxylate shift in zinc enzymes: A computational study". Journal of the American Chemical Society 129 5 (2007): 1378-1385.
    10.1021/ja067103n
  302. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Unravelling Hot Spots: a comprehensive computational mutagenesis study". Theoretical Chemistry Accounts 117 1 (2007): 99-113.
    10.1007/s00214-006-0151-z
  303. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Theoretical studies on farnesyltransferase: The distances paradox explained". Proteins-Structure Function and Bioinformatics 66 1 (2007): 205-218.
    10.1002/prot.21219
  304. Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. L.. "Understanding ribonucleotide reductase inactivation by gemcitabine". Chemistry-a European Journal 13 30 (2007): 8507-8515.
    10.1002/chem.200700260
  305. 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
  306. da Fonseca, R.; Melo, A.; Iori, F.; Menziani, C.; Ramos, M.J.. "Molecular interactions between human cytochrome P450 1A2 and flavone derivatives". Medicinal Chemistry 2 4 (2006): 401-406. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746110349&partnerID=MN8TOARS.
    10.2174/157340606777723988
  307. Marques, A. T.; Antunes, A.; Fernandes, P. A.; Ramos, M. J.. "Comparative evolutionary genomics of the HADH2 gene encoding A beta-binding alcohol dehydrogenase/17 beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10)". Bmc Genomics 7 (2006):
    10.1186/1471-2164-7-202
  308. Pereira, S.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Computational studies on class I ribonucleotide reductase: Understanding the mechanisms of action and inhibition of a cornerstone enzyme for the treatment of cancer". European Biophysics Journal with Biophysics Letters 35 2 (2006): 125-135.
    10.1007/s00249-005-0026-6
  309. Ramos, M. J.; Fernandes, P. A.. "Atomic-Level Rational Drug Design". Current Computer-Aided Drug Design 2 1 (2006): 57-81.
    10.2174/157340906776056464
  310. Sharma, R. K.; Chopra, S.; Sharma, S. D.; Pande, V.; Ramos, M. J.; Meguro, K.; Inoue, J. I.; Otsuka, M.. "Biological evaluation, chelation, and molecular modeling studies of novel metal-chelating inhibitors of NF-kappa B-DNA binding: Structure activity relationships". Journal of Medicinal Chemistry 49 12 (2006): 3595-3601.
    10.1021/jm050617x
  311. Cerqueira, Nmfsa; Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "Dehydration of ribonucleotides catalyzed by ribonucleotide reductase: The role of the enzyme". Biophysical Journal 90 6 (2006): 2109-2119.
    10.1529/biophysj.104.054627
  312. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Detailed microscopic study of the full ZipA : FtsZ interface". Proteins-Structure Function and Bioinformatics 63 4 (2006): 811-821.
    10.1002/prot.20944
  313. Henriques, E. S.; Nascimento, M. A. C.; Ramos, M. J.. "Computational study of some benzamidine-based inhibitors of thrombin-like snake venom proteinases". International Journal of Quantum Chemistry 106 9 (2006): 2107-2121.
    10.1002/qua.20999
  314. Branco, R. J. F.; Fernandes, P. A.; Ramos, M. J.. "Cu, Zn Superoxide dismutase: distorted active site binds substrate without significant energetic cost". Theoretical Chemistry Accounts 115 1 (2006): 27-31.
    10.1007/s00214-005-0672-x
  315. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "Theoretical study of the unusual protonation properties of the active site cysteines in thioredoxin". Journal of Physical Chemistry B 110 11 (2006): 5758-5761.
    10.1021/jp053275f
  316. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Unraveling the importance of protein-protein interaction: Application of a computational alanine-scanning mutagenesis to the study of the IgG1 streptococcal protein G (C2 fragment) complex". Journal of Physical Chemistry B 110 22 (2006): 10962-10969.
    10.1021/jp054760d
  317. Santos, H. R. R.; Ujaque, G.; Ramos, M. J.; Gomes, Janf. "QM/QM study of the coverage effects on the adsorption of amino-cyclopentene at the Si(100) surface". Journal of Computational Chemistry 27 15 (2006): 1892-1897.
    10.1002/jcc.20513
  318. Carvalho, A. P.; Fernandes, P. A.; Ramos, M. J.. "Similarities and differences in the thioredoxin superfamily". Progress in Biophysics & Molecular Biology 91 3 (2006): 229-248.
    10.1016/j.pbiomolbio.2005.06.012
  319. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "Insights on resistance to reverse transcriptase: The different patterns of interaction of the nucleoside reverse transcriptase inhibitors in the deoxyribonucleotide triphosphate binding site relative to the normal substrate". Journal of Medicinal Chemistry 49 26 (2006): 7675-7682.
    10.1021/jm060698c
  320. Fernandes, P. A.; Araujo, Mlac; Barbosa, A. J. M.; Alves, C. N.; Ferreira, Z. Q.; Gonzalez, C. R. N.; Lima, Cfrac; et al. "Lead optimisation: Improving the affinity of the antiretrovirals Nelfinavir and Amprenavir for HIV-1 protease". Letters in Drug Design & Discovery 3 6 (2006): 383-389.
    10.2174/157018006777805576
  321. Carvalho, A. T. P.; Fernandes, P. A.; Ramos, M. J.. "Determination of the Delta pKa between the active site cysteines of thioredoxin and DsbA". Journal of Computational Chemistry 27 8 (2006): 966-975.
    10.1002/jcc.20404
  322. Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Enzyme ribonucleotide reductase: Unraveling an enigmatic paradigm of enzyme inhibition by furanone derivatives". Journal of Physical Chemistry B 110 42 (2006): 21272-21281.
    10.1021/jp0608269
  323. Carvalho, A. P.; Fernandes, P. A.; Ramos, M. J.. "Molecular insights into the mechanisms of HIV-1 reverse transcriptase resistance to nucleoside analogs". Mini-Reviews in Medicinal Chemistry 6 5 (2006): 549-555.
    10.2174/138955706776876276
  324. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Protein-ligand docking: Current status and future challenges". Proteins-Structure Function and Bioinformatics 65 1 (2006): 15-26.
    10.1002/prot.21082
  325. Lucas, M. F.; Ramos, M. J.. "Mechanism of a soluble fumarate reductase from Shewanella frigidimarina: A theoretical study". Journal of Physical Chemistry B 110 21 (2006): 10550-10556.
    10.1021/jp057456t
  326. Branco, R. J. F.; Fernandes, P. A.; Ramos, M. J.. "Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase". Journal of Physical Chemistry B 110 33 (2006): 16754-16762.
    10.1021/jp056855l
  327. Ramos, M. J.; Fernandes, P. A.. "Computer modeling and research in the classroom". Journal of Chemical Education 82 7 (2005): 1021-1025. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000229773400017&KeyUID=WOS:000229773400017.
  328. da Fonseca, R.; Marini, M.; Melo, A.; Menziani, M. C.; Ramos, M. J.. "Computational Insight into Anti-mutagenic Properties of CYP1A Flavonoid Ligands". Medicinal Chemistry 1 4 (2005): 355-360. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000208266000004&KeyUID=WOS:000208266000004.
    10.2174/1573406054368729
  329. Pande, V.; Ramos, M.J.. "NF-¿B in human disease: Current inhibitors and prospects for De Novo structure based design of inhibitors". Current Medicinal Chemistry 12 3 (2005): 357-374. http://www.scopus.com/inward/record.url?eid=2-s2.0-14544269951&partnerID=MN8TOARS.
  330. Fernandes, P. A.; Maia, A. R. R.; Almeida, A. A. S.; Silva, B. F. B.; Ribeiro, C. M. S.; Ribeiro, C. F. B.; Ribeiro, D. S. M.; et al. "New designs for inhibitors of the NF-kappa B: DNA binding". Theoretical Chemistry Accounts 113 4 (2005): 197-204.
    10.1007/s00214-005-0628-1
  331. Preto, M. A. C.; Melo, A.; Maia, H. L. S.; Mavromoustakos, T.; Ramos, M. J.. "Molecular dynamics simulations of angiotensin II in aqueous and dimethyl sulfoxide environments". Journal of Physical Chemistry B 109 37 (2005): 17743-17751.
    10.1021/jp0521048
  332. Pande, V.; Ramos, M. J.. "Molecular recognition of 15-deoxy-Delta(12,14)-prostaglandin J(2) by nuclear factor-kappa B and other cellular proteins". Bioorganic & Medicinal Chemistry Letters 15 18 (2005): 4057-4063.
    10.1016/j.bmcl.2005.06.025
  333. Ramos, M. J.; Magalhaes, A. L.; Melo, A. S.; Fernandes, P. A.. "Special issue: A collection of papers presented at the 30th international congress of theoretical chemists of Latin Expression, Porto, Portugal, 8-12 September 2004 - Foreword". Journal of Molecular Structure-Theochem 729 1-2 (2005): VII-VII.
    10.1016/j.theochem.2005.04.028
  334. Pande, V.; Ramos, M. J.. "Structural basis for the GSK-3 beta binding affinity and selectivity against CDK-2 of 1-(4-aminofurazan-3yl)-5-dialkylaminomethyl-1-H- 1,2,3 triazole-4-carboxylic acid derivatives". Bioorganic & Medicinal Chemistry Letters 15 23 (2005): 5129-5135.
    10.1016/j.bmcl.2005.08.077
  335. Cerqueira, Nmfsa; Pereira, S.; Fernandes, P. A.; Ramos, M. J.. "Overview of ribonucleotide reductase inhibitors: An appealing target in anti-tumour therapy". Current Medicinal Chemistry 12 11 (2005): 1283-1294.
    10.2174/0929867054020981
  336. Branco, R. J. F.; Fernandes, P. A.; Ramos, M. J.. "Density-functional calculations of the Cu, Zn superoxide dismutase redox potential: The influence of active site distortion". Journal of Molecular Structure-Theochem 729 1-2 (2005): 141-146.
    10.1016/j.theochem.2004.12.046
  337. Silva, P. J.; Ramos, M. J.. "Density-functional study of mechanisms for the cofactor-free decarboxylation performed by uroporphyrinogen III decarboxylase". Journal of Physical Chemistry B 109 38 (2005): 18195-18200.
    10.1021/jp051792s
  338. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Farnesyltransferase: Theoretical studies on peptide substrate entrance thiol or thiolate coordination?". Journal of Molecular Structure-Theochem 729 1-2 (2005): 125-129.
    10.1016/j.theochem.2005.03.022
  339. Sharma, R. K.; Pande, V.; Ramos, M. J.; Rajor, H. K.; Chopra, S.; Meguro, K.; Inoue, J.; Otsuka, M.. "Inhibitory activity of polyhydroxycarboxylate chelators against recombinant NF-kappa B p50 protein-DNA binding". Bioorganic Chemistry 33 2 (2005): 67-81.
    10.1016/j.bioorg.2004.12.001
  340. Antunes, A.; Ramos, M. J.. "Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes". Genomics 86 6 (2005): 708-717.
    10.1016/j.ygeno.2005.08.002
  341. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Farnesyltransferase - New insights into the zinc-coordination sphere paradigm: Evidence for a carboxylate-shift mechanism". Biophysical Journal 88 1 (2005): 483-494.
    10.1529/biophysj.104.048207
  342. Pereira, S.; Fernandes, P. A.; Ramos, M. J.. "Theoretical study on the inhibition of ribonucleotide reductase by 2 '-mercapto-2 '-deoxyribonucleoside-5 '-diphosphates". Journal of the American Chemical Society 127 14 (2005): 5174-5179.
    10.1021/ja046662w
  343. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Unraveling the mechanism of the farnesyltransferase enzyme". Journal of Biological Inorganic Chemistry 10 1 (2005): 3-10.
    10.1007/s00775-004-0612-6
  344. Iori, F.; da Fonseca, R.; Ramos, M. J.; Menziani, M. C.. "Theoretical quantitative structure-activity relationships of flavone ligands interacting with cytochrome P450 1A1 and 1A2 isozymes". Bioorganic & Medicinal Chemistry 13 14 (2005): 4366-4374.
    10.1016/j.bmc.2005.04.066
  345. Lucas, M. D.; Ramos, M. J.. "Theoretical study of the suicide inhibition mechanism of the enzyme pyruvate formate lyase by methacrylate". Journal of the American Chemical Society 127 18 (2005): 6902-6909.
    10.1021/ja047699j
  346. Santos, H. R. R.; Ramos, M. J.; Gomes, Janf. "Adsorption of protected and unprotected amino-cyclopentene at the Si(100) surface modeled with a hybrid quantum mechanical cluster technique". Physical Review B 72 7 (2005):
    10.1103/physrevb.72.075445
  347. Santos, H. R. R.; Ramos, M. J.; Gomes, Janf. "A new strategy to model the Si(100) surface". Comptes Rendus Chimie 8 9-10 (2005): 1461-1468.
    10.1016/j.crci.2004.10.033
  348. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Accuracy of the numerical solution of the Poisson-Boltzmann equation". Journal of Molecular Structure-Theochem 729 1-2 (2005): 11-18.
    10.1016/j.theochem.2004.12.049
  349. Ramos, M. J.; Fernandes, P. A.; Melo, A.. "Modeling chemical and biological systems: A successful course for undergraduate students". Journal of Chemical Education 81 1 (2004): 72-75. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000187308400030&KeyUID=WOS:000187308400030.
    10.1021/ed081p72
  350. Henriques, E. S.; Fonseca, N.; Ramos, M. J.. "On the modeling of snake venom serine proteinase interactions with benzamidine-based thrombin inhibitors". Protein Science 13 9 (2004): 2355-2369.
    10.1110/ps.04746804
  351. Cerqueira, Nmfsa; Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzyme". Journal of Computational Chemistry 25 16 (2004): 2031-2037.
    10.1002/jcc.20127
  352. Cerqueira, Nmfsa; Femandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "New insights into a critical biological control step of the mechanism of Ribonucleotide reductase". Journal of Molecular Structure-Theochem 709 1-3 (2004): 53-65.
    10.1016/j.theochem.2003.10.073
  353. Fernandes, P. A.; Ramos, M. J.. "Theoretical insights into the mechanism for thiol/disulfide exchange". Chemistry-a European Journal 10 1 (2004): 257-266.
    10.1002/chem.200305343
  354. Pereira, S.; Fernandes, P. A.; Ramos, M. J.. "Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2 '-azido-2 '-deoxyribonucleoside 5-diphosphates". Journal of Computational Chemistry 25 2 (2004): 227-237.
    10.1002/jcc.10375
  355. Sharma, R. K.; Otsuka, M.; Pande, V.; Inoue, J.; Ramos, M. J.. "Evans Blue is an inhibitor of nuclear factor-kappa B (NF-kappa B)-DNA binding". Bioorganic & Medicinal Chemistry Letters 14 24 (2004): 6123-6127.
    10.1016/j.bmcl.2004.07.096
  356. Pereira, S.; Fernandes, P. A.; Ramos, M. J.. "Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine". Journal of Computational Chemistry 25 10 (2004): 1286-1294.
    10.1002/jcc.20054
  357. Portela, C.; Afonso, C. M. M.; Pinta, M. M. M.; Ramos, M. J.. "Definition of an electronic profile of compounds with inhibitory activity against hematin aggregation in malaria parasite". Bioorganic & Medicinal Chemistry 12 12 (2004): 3313-3321.
    10.1016/j.bmc.2004.03.060
  358. Fernandes, P. A.; Cruz, A. I. S.; Maia, A. R. R.; Almeida, A. A. S.; da Silva, A. M. N.; Silva, B. F. B.; Ribeiro, C. M. S.; et al. "Design of 2-cyclopentenone derivatives with enhanced NF-kappa B: DNA binding inhibitory properties". Journal of Molecular Structure-Theochem 685 1-3 (2004): 73-82.
    10.1016/j.theochem.2004.06.027
  359. Fernandes, P. A.; Ramos, M. J.. "Theoretical studies on the mode of inhibition of ribonucleotide reductase by 2 '-substituted substrate analogues". Chemistry-a European Journal 9 23 (2003): 5916-5925.
    10.1002/chem.200304948
  360. Henriques, E. S.; Bastos, M.; Geraldes, Cfgc; Ramos, M. J.. "Studies of inclusion complexes between cyclodextrins and polyazamacrocyclic chelates of lanthanide(III) ions". Journal of Chemical Thermodynamics 35 10 (2003): 1717-1735.
    10.1016/s0021-9614(03)00160-5
  361. Fernandes, P. A.; Ramos, M. J.. "Theoretical studies on the mechanism of inhibition of ribonucleotide reductase by (E)-2 '-fluoromethylene-2 '-deoxycitidine-5 '-diphosphate". Journal of the American Chemical Society 125 20 (2003): 6311-6322.
    10.1021/ja0208613
  362. Da Fonseca, R.; Menziani, M. C.; Melo, A.; Ramos, M. J.. "Modelling the metabolic action of human and rat CYP1A2 and its relationship with the carcinogenicity of heterocyclic amines". Molecular Physics 101 17 (2003): 2731-2741.
    10.1080/00268970310001603112
  363. Fernandes, P. A.; Carvalho, A. T. P.; Marques, A. T.; Pereira, A. L. F.; Madeira, A. P. S.; Ribeiro, A. S. P.; Carvalho, A. F. R.; et al. "New designs for MRI contrast agents". Journal of Computer-Aided Molecular Design 17 7 (2003): 463-473.
    10.1023/A:1027347527385
  364. Portela, C.; Afonso, C. M. M.; Pinto, M. M. M.; Ramos, M. J.. "Computational studies of new potential antimalarial compounds - Stereoelectronic complementarity with the receptor". Journal of Computer-Aided Molecular Design 17 9 (2003): 583-595.
    10.1023/b:jcam.0000005754.24588.a0
  365. Henriques, E. S.; Geraldes, Cfgc; Ramos, M. J.. "Modelling studies in aqueous solution of lanthanide (III) chelates designed for nuclear magnetic resonance biomedical applications". Molecular Physics 101 15 (2003): 2319-2333.
    10.1080/0026897031000108023
  366. Lucas, M. D.; Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "Pyruvate formate lyase: A new perspective". Journal of Physical Chemistry B 107 24 (2003): 5751-5757.
    10.1021/jp0223096
  367. Portela, C.; Afonso, C. M. M.; Pinto, M. M. M.; Ramos, M. J.. "Receptor-drug association studies in the inhibition of the hematin aggregation process of malaria". Febs Letters 547 1-3 (2003): 217-222.
    10.1016/s0014-5793(03)00692-6
  368. Pande, V.; Ramos, M. J.. "Nuclear Factor Kappa B: A potential target for anti-HIV chemotherapy". Current Medicinal Chemistry 10 16 (2003): 1603-1615.
    10.2174/0929867033457250
  369. Preto, M. A. C.; Melo, A.; Costa, S. P. G.; Maia, H. L. S.; Ramos, M. J.. "Parametrization of synthetic amino acids". Journal of Physical Chemistry B 107 51 (2003): 14556-14562.
    10.1021/jp030544y
  370. Pande, V.; Sharma, R. K.; Inoue, J. I.; Otsuka, M.; Ramos, M. J.. "A molecular modeling study of inhibitors of nuclear factor kappa-B (p50) - DNA binding". Journal of Computer-Aided Molecular Design 17 12 (2003): 825-836.
    10.1023/b:jcam.0000021835.72265.63
  371. Silva, P. J.; Fernandes, P. A.; Ramos, M. J.. "A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase". Theoretical Chemistry Accounts 110 5 (2003): 345-351.
    10.1007/s00214-003-0476-9
  372. Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "The reduction of ribonucleotides catalyzed by the enzyme ribonucleotide reductase". Theoretical Chemistry Accounts 108 6 (2002): 352-364.
    10.1007/s00214-002-0393-3
  373. Melo, A.; Ramos, M. J.. "Theoretical study of the amino acid interactions in the binding region of the trypsin-pancreatic trypsin inhibitor complex". Journal of Molecular Structure-Theochem 580 (2002): 251-262.
    10.1016/S0166-1280(01)00621-2
  374. Henriques, E. S.; Floriano, W. B.; Reuter, N.; Melo, A.; Brown, D.; Gomes, Janf; Maigret, B.; Nascimento, M. A. C.; Ramos, M. J.. "The search for a new model structure of beta-Factor XIIa". Journal of Computer-Aided Molecular Design 15 4 (2001): 309-322.
    10.1023/a:1011128521816
  375. Melo, A.; Puga, A. T.; Gentil, F.; Brito, N.; Alves, A. P.; Ramos, M. J.. "Byte structure variable length coding (BS-VLC): A new specific algorithm applied in the compression of trajectories generated by molecular dynamics". Journal of Chemical Information and Computer Sciences 40 3 (2000): 559-566.
    10.1021/ci990069u
  376. Magalhaes, AL; Maigret, B; Gomes, JANF; Ramos, MJ. "Hybrid QM/MM study of a fundamental biological interaction surrounded by its protein environment". INTERNET JOURNAL OF CHEMISTRY (2000):
  377. Magalhaes, A. L.; Madail, Srrs; Ramos, M. J.. "Prediction of the Raman spectrum of the aqueous formate anion by a combined density functional theory and self-consistent-reaction-field study". Theoretical Chemistry Accounts 105 1 (2000): 68-76.
    10.1007/s002140000187
  378. Melo, A.; Ramos, M. J.; Floriano, W. B.; Gomes, Janf; Leao, J. F. R.; Magalhaes, A. L.; Maigret, B.; Nascimento, M. C.; Reuter, N.. "Theoretical study of arginine-carboxylate interactions". Journal of Molecular Structure-Theochem 463 1-2 (1999): 81-90. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000079425800012&KeyUID=WOS:000079425800012.
    10.1016/s0166-1280(98)00396-0
  379. Melo, A.; Ramos, M. J.. "A new partitioning scheme for molecular interacting systems within a multiconfigurational or monoconfigurational Hartree-Fock formalism". International Journal of Quantum Chemistry 72 3 (1999): 157-176.
    10.1002/(sici)1097-461x(1999)72:3<157::aid-qua1>3.3.co;2-#
  380. Henriques, E. S.; Bastos, M.; Geraldes, Cfgc; Ramos, M. J.. "Computational approaches to the study of some lanthanide (III) - Polyazamacrocyclic chelates for magnetic resonance imaging". International Journal of Quantum Chemistry 73 2 (1999): 237-248.
    10.1002/(sici)1097-461x(1999)73:2<237::aid-qua17>3.3.co;2-n
  381. Ramos, M. J.; Melo, A.; Henriques, E. S.; Gomes, Janf; Reuter, N.; Maigret, B.; Floriano, W. B.; Nascimento, M. A. C.. "Modeling enzyme-inhibitor interactions in serine proteases". International Journal of Quantum Chemistry 74 3 (1999): 299-314.
    10.1002/(sici)1097-461x(1999)74:3<299::aid-qua3>3.0.co;2-k
  382. Henriques, E. F.; Ramos, M. J.; Reynolds, C. A.. "Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein". Journal of Computer-Aided Molecular Design 11 6 (1997): 547-556. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000071973800003&KeyUID=WOS:000071973800003.
    10.1023/a:1007919812771
  383. Bastos, M.; Afonso, M.; Cacote, M. H. M.; Ramos, M. J.. "Interactions in the model system alpha-cyclodextrin-glycerol - Experimental and theoretical study". Journal of the Chemical Society-Faraday Transactions 93 11 (1997): 2061-2067.
    10.1039/a608163k
  384. Melo, A.; Ramos, M. J.. "The nature of trypsin-pancreatic trypsin inhibitor binding: Free energy calculation of Tys(39)->Phe(39) mutation in trypsin". Journal of Peptide Research 50 5 (1997): 382-387. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:A1997YC65100009&KeyUID=WOS:A1997YC65100009.
  385. Melo, A.; Ramos, M. J.. "PROTON-TRANSFER IN ARGININE-CARBOXYLATE INTERACTIONS". Chemical Physics Letters 245 4-5 (1995): 498-502.
    10.1016/0009-2614(95)01058-H
  386. Ramos, M.J.; Richards, W.G.. "Computer models of beta-factor XIIa and inhibitor". Drug News and Perspectives 5 6 (1992): 325-330. http://www.scopus.com/inward/record.url?eid=2-s2.0-0026730608&partnerID=MN8TOARS.
  387. Ramos, M. J.. "MODEL STRUCTURE FOR THE HUMAN BLOOD-COAGULATION AGENT BETA-FACTOR XIIA". Journal of Molecular Graphics 9 2 (1991): 91-&.
    10.1016/0263-7855(91)85004-i
  388. Lopes de Magalhães, A; Ramos, MJ; Lopes de Magalhães, A.; Ramos, M.J.. "Calculation of hyperfine coupling constants of muonated radicals". Chemical Physics Letters 165 6 (1990): 528-534. https://www.authenticus.pt/P-00H-5S1.
    10.1016/0009-2614(90)87033-n
  389. RAMOS, MJ. "MUON CHEMISTRY AND MU-SR". JOURNAL DE CHIMIE PHYSIQUE ET DE PHYSICO-CHIMIE BIOLOGIQUE (1987): https://www.authenticus.pt/P-001-V7C.
  390. Webster, B.; Hilczer, M.; Ramos, M. J.; Carmichael, I.. "THE INCLUSION OF D-TYPE GAUSSIAN FUNCTIONS IN THE ANALYTIC METHOD FOR THE CALCULATION OF ELECTROSTATIC MOLECULAR POTENTIALS - INTERACTION OF A PROTON OR A POSITIVE MUON WITH CARBON-MONOXIDE". Journal of the Chemical Society-Faraday Transactions Ii 81 (1985): 1761-1769.
    10.1039/f29858101761
  391. Amaral, A.; Gomes, J.A.N.F.; Ramos, M.. "Preface". Journal of Molecular Structure: THEOCHEM 120 C (1985): http://www.scopus.com/inward/record.url?eid=2-s2.0-46549104257&partnerID=MN8TOARS.
  392. Ramos, M. J.; McKenna, D.; Webster, B. C.; Roduner, E.. "MUON SPIN ROTATION SPECTRA FOR MUONIUM ISOTOPICALLY SUBSTITUTED ETHYL RADICALS". Journal of the Chemical Society-Faraday Transactions I 80 (1984): 255-265.
    10.1039/F19848000255
  393. Ramos, M. J.; McKenna, D.; Webster, B. C.; Roduner, E.. "THE BARRIERS TO INTERNAL-ROTATION FOR MUONIC-SUBSTITUTED ETHYL RADICALS". Journal of the Chemical Society-Faraday Transactions I 80 (1984): 267-274.
    10.1039/F19848000267
  394. Ramos, M. J.; Webster, B.. "AN ANALYTIC METHOD FOR THE CALCULATION OF ELECTROSTATIC MOLECULAR POTENTIALS". Journal of the Chemical Society-Faraday Transactions Ii 79 (1983): 1389-1398.
    10.1039/f29837901389
  395. Roduner, E.; Strub, W.; Burkhard, P.; Hochmann, J.; Percival, P. W.; Fischer, H.; Ramos, M.; Webster, B. C.. "MUONIUM SUBSTITUTED ORGANIC FREE-RADICALS IN LIQUIDS - MUON ELECTRON HYPERFINE COUPLING-CONSTANTS OF ALKYL AND ALLYL RADICALS". Chemical Physics 67 3 (1982): 275-285.
    10.1016/0301-0104(82)85189-6
Capítulo de livro
  1. Maria Joao Ramos. "BOOK CHAPTERS - I have published 11 book chapters. For details please see www.fc.up.pt/pessoas/mjramos/BOOK _CHAPTERS.pdf". 2022.
  2. Teixeira, CSS; Fernandes, HS; Fernandes, PA; Ramos, MJ; Cerqueira, NMFSA. "Cancer therapies based on enzymatic amino acid depletion". 2017.
    10.1016/b978-0-323-46144-3.00024-6
  3. Sousa, Sergio F.; Coimbra, Joao T. S.; Fernandes, Pedro A.; Marino, Tiziana; Ramos, Maria J.; Russo, Nino; Nascimento, MAC; et al. "Molecular Dynamics Analysis of FAAH Complexed with Anandamide". 114-130. 2015.
    10.1007/978-3-319-14397-2_7
  4. Piekarski, D. G.; Ramos, M. J.; Diaz-Tendero, S.; Diaz, C; Rabadan, I; Garcia, G; Mendez, L; Martin, F. "Dynamics of excited clusters of beta-alanine in the gas phase". 2015.
    10.1088/1742-6596/635/3/032089
  5. Brás, NF; Coimbra, JTS; Neves, RPP; Cerqueira, NMFSA; Sousa, SF; Fernandes, PA; Ramos, MJ. "Computational Biochemistry". 2013.
    10.1016/b978-0-12-409547-2.10833-9
  6. Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ. "Ribonucleotide Reductase – Computational Studies". 2013.
    10.1007/978-3-642-16712-6_264
  7. Sousa, SF; Fernandes, PA; Ramos, MJ. "Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes". 2010.
    10.1007/978-90-481-3034-4_11
  8. Moreira, IS; Fernandes, PA; Ramos, MJ. "Computational Determination of the Relative Free Energy of Binding – Application to Alanine Scanning Mutagenesis". 2007.
    10.1007/1-4020-5372-x_6
Livro
  1. Brás, N.F.; Cerqueira, N.M.F.S.A.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. Protein ligand docking in drug discovery. 2014.
    10.1007/978-3-319-09976-7_11
  2. Ramos, M.J.; Melo, A.; Henriques, E.S.; Ramos, MJ; Melo, A; Henriques, ES. Modelling enzyme - Ligand interactions. 2001.
Resumo em conferência
  1. Sousa, CF; Coimbra, JT; Ramose, MJ; Fernandes, PA; Gameiro, P; Ramos, MJ. "Combining theoretical and experimental approaches to understand the mechanism of antibiotic permeation: implications on the fight against bacterial resistance". 2019.
  2. Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ. "Enzyme Ribonucleotide Reductase. The Paradigm of Enzyme Inhibition by Furanone Derivatives". 2005.
    10.1107/s0108767305079511

Outros

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

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2020 PLENARIES/INVITED TALKS - I have been invited to deliver 120 Invited Talks / Plenaries in International Conferences. Details for 2020-1986 are given in www.fc.up.pt/pessoas/mjramos/PLENARIES_INVITED_TALKS.pdf

Orientação

Título / Tema
Papel desempenhado 		Curso (Tipo)
Instituição / Organização
2020 - Atual SUPERVISION OF SCIENTIFIC RESEARCHERS - I supervise/have supervised 6 Senior Researchers (I.A.), 8 Post-Docs, 35 PhD. students, 21 M.Sc. students, 18 Research Grant Students (B.I.), 3 Research Initiation Grant Students (B.I.I.) and 58 last year Undergraduate Research Project Students (Chemistry and Biochemistry) - for more details on names please consult www.fc.up.pt/pessoas/mjramos/SUPERVISION_OF_SCIENTIFIC_RESEARCHERS.pdf
Orientador

Júri de grau académico

Tema
Tipo de participação 		Nome do candidato (Tipo de grau)
Instituição / Organização
2020 PARTICIPATION IN ACADEMIC JURIS - Details on International and national PhD juris are given in www.fc.up.pt/pessoas/mjramos/ACADEMIC_JURIS.pdf National and international cademic juris (Doutoramento)

Arbitragem científica em revista

Nome da revista (ISSN) Editora
2020 - Atual REVIEWING - I have been a reviewer for many scientific journals. Details are given in www.fc.up.pt/pessoas/mjramos/REVIEWING.pdf

Comissão de avaliação

Descrição da atividade
Tipo de assessoria 		Instituição / Organização Entidade financiadora
2000 - 2020 EVALUATION WORK - I have been an evaluator of research projects / university positions / universities, for many years now. Details for 2020-2000 are given in www.fc.up.pt/pessoas/mjramos/EVALUATION_WORK.pdf

Consultoria / Parecer

Descrição da atividade Instituição / Organização
1999 - 2020 RESEARCH INTERESTS - I am/have been a consultant for several companies and my research interests are given in more detail in www.fc.up.pt/pessoas/mjramos/RESEARCH_INTERESTS.pdf
Distinções

Prémio

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