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António M. Baptista graduated in Biochemistry from the University of Lisbon, Portugal, in 1988, where he then stayed until 1990 as a graduate student in Computational Chemistry. He then moved to the University of Porto, Portugal, where he was junior lecturer and member of the Theoretical Chemistry Group until 1991. From 1992 to 1995 he was a PhD student at the Magnetic Resonance Center of SINTEF Unimed, Trondheim, Norway, and then at Instituto de Tecnologia Quimica e Biologica, Portugal, where he completed a PhD degree in Biochemistry in 1998. He then stayed at Instituto de Tecnologia Quimica e Biologica, Portugal, first as a post-doc (1998-2003) and then as Assistant Investigator (2003-2013) and Principal Investigator (since 2014). He is head of the Molecular Simulation lab since 2003, working mainly on electrostatic processes in proteins (especially constant-pH molecular dynamics), and also protein misfolding, proteins in non-aqueous solvents, and peptide dendrimers, among others. Since its formation, the group comprises 3-6 members at a time, including master students, graduate students, PhD students and Post-Docs. He supervised 8 master students, 6 graduate students, 6 PhD students and 4 Post-Docs. He published around 90 articles in international peer-reviewed SCI journals and 4 in books, with a total of 4447 citations, an average of 50 citations per article and an h-index of 37 (Google Scholar, 2024-01-31). He regularly publishes in J. Chem. Theory Comput., J. Phys. Chem. B, J. Chem. Inf. Model., Biophys. J., Proteins, etc, which are among the top journals for modeling/simulation studies, and has also published in J. Am. Chem. Soc., J. Phys. Chem. Lett. and BBA - Bioenergetics. He presented 33 invited talks (the most relevant listed in section "Activities") and is co-author in around 150 other oral or poster communications at scientific conferences. After his PhD, he participated in 12 funded research projects, being the PI in 5 of them. His main expertise is the development and application of theoretical and computational methods to study protein electrostatics, especially constant-pH molecular dynamics methods for molecular simulation, in which he played a pioneering role, publishing the first methods using either continuous or discrete protonation variables, as well as the inclusion of ionic strength effects and proton isomerism. Some of this work has been done in collaboration with other modeling and experimental groups, both national and international (Milan, Berlin, Bern, Aalborg, Bilbao, Marseille, Amsterdam, etc). Since 2008, he is a regular invited speaker in the Workshop on Protein Electrostatics taking place at Telluride, CO, USA, which brings together the major workers in the field, both modelers and experimentalists, who have associated under the pKa Cooperative (http://www.pkacoop.org), organized to advance the development of accurate and useful computational methods for structure-based calculation of pKa values and electrostatic energy in proteins. In 2014 he organized the first Protein Electrostatics Conference, in Lisbon, which has since then been taking place regularly in Europe (Berlin 2016, Belgrade 2018, Genoa 2021 and 2023), usually with him as member of the Scientific Committee.
Identificação

Identificação pessoal

Nome completo
António Manuel Simões Carrão Albuquerque Baptista

Nomes de citação

  • Baptista, António M.

Identificadores de autor

Ciência ID
7213-A81D-F812
ORCID iD
0000-0002-7044-1210
Google Scholar ID
qV4DT_UAAAAJ
Researcher Id
C-7246-2012
Scopus Author Id
57197753768

Domínios de atuação

  • Ciências Exatas - Química - Química Física
  • Ciências Naturais - Ciências Biológicas - Biofísica

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português (Idioma materno)
Inglês Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Francês Utilizador independente (B1) Utilizador independente (B1) Utilizador elementar (A1) Utilizador independente (B1)
Espanhol; Castelhano Utilizador independente (B1) Utilizador independente (B1) Utilizador independente (B1)
Formação
Grau Classificação
1998
Concluído
Biochemistry (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
"Theoretical methods for the simulation of proteins at constant pH" (TESE/DISSERTAÇÃO)
Aprovado por unanimidade
1988
Concluído
Bioquímica (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Alguns aspectos da caracterização de mutantes citoplásmicos em Coprinus cinereus" (TESE/DISSERTAÇÃO)
15
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento
Empregador
2014/02/01 - Atual Investigador principal (carreira) (Investigação) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2003/05/01 - 2014/01/31 Investigador Auxiliar (carreira) (Investigação) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1998/07/01 - 2003/04/30 Pós-doutorado (Investigação) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1997/08/01 - 1998/06/30 Investigador (Investigação) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento
Empregador
1990/06/01 - 1991/12/15 Assistente Estagiário (Docente Universitário) Universidade do Porto Faculdade de Ciências, Portugal

Outros

Categoria Profissional
Instituição de acolhimento
Empregador
1992/01/01 - 1995/12/31 PhD student SINTEF, Noruega
1989/01/01 - 1990/05/31 Graduate student Universidade de Lisboa Faculdade de Ciências, Portugal
1987/10/01 - 1988/10/31 Undergraduate student (estágio de licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
Projetos

Bolsa

Designação Financiadores
2019 - 2022 Modelling pH effects on beta-lactoglobulin using state-of-the-art constant-pH molecular dynamics
PTDC/QUI-OUT/29441/2017
Investigador
Fundação para a Ciência e a Tecnologia
2016 - 2019 CpHMD-L simulations of pHLIP peptides: design of new tumor-targeted drug delivery systems
PTDC/QEQ-COM/5904/2014
Investigador
Fundação para a Ciência e a Tecnologia
2013 - 2015 Increasing the realism of membrane modelling in constant-pH molecular dynamics methods: inclusion of electrochemical gradients and lipid titration
PTDC/QEQ-COM/1623/2012
Investigador responsável
Fundação para a Ciência e a Tecnologia
2011 - 2014 Proton transfer and proton pumping in haem-copper oxidases. Methodological developments and their application to unravel the molecular mechanism
PTDC/QUI-BIQ/113446/2009
Investigador
Fundação para a Ciência e a Tecnologia
2011/01/01 - 2013 Adding realism to the molecular modeling of lipidic membranes: inclusion of pH effects Fundação para a Ciência e a Tecnologia
2010 - 2013 Study of pH-dependent protein misfolding using state-of-the-art molecular modeling methods
PTDC/QUI-BIQ/105238/2008
Investigador responsável
Fundação para a Ciência e a Tecnologia
2010 - 2013 Including protonation effects in the simulation of peptides and proteins in membrane environments
PTDC/BIA-PRO/104378/2008
Investigador responsável
Fundação para a Ciência e a Tecnologia
2010 - 2013 Understanding structure-activity relationships in peptide dendrimers using a molecular modelling approach
PTDC/QUI-QUI/100416/2008
Investigador responsável
Fundação para a Ciência e a Tecnologia
2003 - 2007 Increasing realism in protein modelling: including pH and redox effects into molecular dynamics simulations
POCTI/BME/45810/2002
Investigador responsável
Fundação para a Ciência e a Tecnologia
2001 - 2003 Molecular modelling of key redox proteins in bacterium metabolism: methodology and applications
POCTI/BME/32789/99
Investigador
Fundação para a Ciência e a Tecnologia
2001 - 2003 Novel respiratory complexes: molecular basis for energy transduction
POCTI/BME/36560/99
Investigador
Fundação para a Ciência e a Tecnologia
2000 - 2002 Structure-function relationships of serine hydrolases in non-conventinal media
PRAXIS/P/BIO/14314/1998
Investigador
Ministério da Ciência Tecnologia e Ensino Superior
Produções

Publicações

Artigo em revista
  1. Lucie da Rocha; António M. Baptista; Sara R. R. Campos. "Computational Study of the pH-Dependent Ionic Environment around ß-Lactoglobulin". The Journal of Physical Chemistry B (2022): https://doi.org/10.1021/acs.jpcb.2c03797.
    10.1021/acs.jpcb.2c03797
  2. António M. Baptista; Lucie da Rocha; Sara R. R. Campos. "FixBox: A General Algorithm to Fix Molecular Systems in Periodic Boxes". Journal of Chemical Information and Modeling (2022): https://doi.org/10.1021/acs.jcim.2c00823.
    10.1021/acs.jcim.2c00823
  3. Lucie da Rocha; António M. Baptista; Sara R. R. Campos. "Correction to “Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of ß-Lactoglobulin”". Journal of Chemical Theory and Computation (2022): https://doi.org/10.1021/acs.jctc.2c00605.
    10.1021/acs.jctc.2c00605
  4. Lucie da Rocha; António M. Baptista; Sara R. R. Campos. "Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of ß-Lactoglobulin". Journal of Chemical Theory and Computation (2022): https://doi.org/10.1021/acs.jctc.1c01187.
    10.1021/acs.jctc.1c01187
  5. Lousa, D.; Pinto, A.R.T.; Campos, S.R.R.; Baptista, A.M.; Veiga, A.S.; Castanho, M.A.R.B.; Soares, C.M.. "Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment". Scientific Reports 10 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85096181420&partnerID=MN8TOARS.
    10.1038/s41598-020-77040-y
  6. Diogo Vila-Viçosa; Pedro B. P. S. Reis; António M. Baptista; Chris Oostenbrink; Miguel Machuqueiro. "A pH Replica Exchange Scheme in the Stochastic Titration Constant-pH MD Method". Journal of Chemical Theory and Computation (2019): https://doi.org/10.1021/acs.jctc.9b00030.
    10.1021/acs.jctc.9b00030
  7. Nicoletta Liguori; Sara R. R. Campos; António M. Baptista; Roberta Croce. "Molecular Anatomy of Plant Photoprotective Switches: The Sensitivity of PsbS to the Environment, Residue by Residue". The Journal of Physical Chemistry Letters (2019): 1737-1742. https://doi.org/10.1021/acs.jpclett.9b00437.
    10.1021/acs.jpclett.9b00437
  8. Pedro B. P. S. Reis; Diogo Vila-Viçosa; Sara R. R. Campos; António M. Baptista; Miguel Machuqueiro. "Role of Counterions in Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimers". ACS Omega (2018): https://doi.org/10.1021/acsomega.7b01708.
    10.1021/acsomega.7b01708
  9. Magalhães, P.R.; Oliveira, A.S.F.; Campos, S.R.R.; Soares, C.M.; Baptista, A.M.. "Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study". Journal of Chemical Information and Modeling 57 2 (2017): 256-266. http://www.scopus.com/inward/record.url?eid=2-s2.0-85014290827&partnerID=MN8TOARS.
    10.1021/acs.jcim.6b00575
  10. Campos, S.R.R.; Iranzo, O.; Baptista, A.M.. "Constant-pH MD Simulations Portray the Protonation and Structural Behavior of Four Decapeptides Designed to Coordinate Cu2+". Journal of Physical Chemistry B 120 6 (2016): 1080-1091. http://www.scopus.com/inward/record.url?eid=2-s2.0-84959440690&partnerID=MN8TOARS.
    10.1021/acs.jpcb.5b12052
  11. Conceição, K.; Magalhães, P.R.; Campos, S.R.R.; Domingues, M.M.; Ramu, V.G.; Michalek, M.; Bertani, P.; et al. "The anti-inflammatory action of the analgesic kyotorphin neuropeptide derivatives: Insights of a lipid-mediated mechanism". Amino Acids 48 1 (2016): 307-318. http://www.scopus.com/inward/record.url?eid=2-s2.0-84955207969&partnerID=MN8TOARS.
    10.1007/s00726-015-2088-9
  12. Filipe, L.C.S.; Campos, S.R.R.; Machuqueiro, M.; Darbre, T.; Baptista, A.M.. "Structuring peptide dendrimers through pH modulation and substrate binding". Journal of Physical Chemistry B 120 38 (2016): 10138-10152. http://www.scopus.com/inward/record.url?eid=2-s2.0-84992322845&partnerID=MN8TOARS.
    10.1021/acs.jpcb.6b05905
  13. Oliveira, A.S.F.; Campos, S.R.R.; Baptista, A.M.; Soares, C.M.. "Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations". Biochimica et Biophysica Acta - Bioenergetics 1857 6 (2016): 759-771. http://www.scopus.com/inward/record.url?eid=2-s2.0-84964689558&partnerID=MN8TOARS.
    10.1016/j.bbabio.2016.03.024
  14. de Barros, D.P.C.; Campos, S.R.R.; Azevedo, A.M.; Baptista, A.M.; Aires-Barros, M.R.. "Predicting protein partition coefficients in aqueous two phase system". Journal of Chromatography A 1470 (2016): 50-58. http://www.scopus.com/inward/record.url?eid=2-s2.0-84995380022&partnerID=MN8TOARS.
    10.1016/j.chroma.2016.09.072
  15. Filipe, L.C.S.; Machuqueiro, M.; Darbre, T.; Baptista, A.M.. "Exploring the Structural Properties of Positively Charged Peptide Dendrimers". Journal of Physical Chemistry B 120 43 (2016): 11323-11330. http://www.scopus.com/inward/record.url?eid=2-s2.0-85032160899&partnerID=MN8TOARS.
    10.1021/acs.jpcb.6b09156
  16. Correia, M.; Snabe, T.; Thiagarajan, V.; Petersen, S.B.; Campos, S.R.R.; Baptista, A.M.; Neves-Petersen, M.T.. "Erratum: Photonic activation of plasminogen induced by low dose UVB (PLoS ONE (2015) 10:12 (e0144794))". PLoS ONE 10 12 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84957109767&partnerID=MN8TOARS.
    10.1371/journal.pone.0144794
  17. Santos, H.A.F.; Vila-Viçosa, D.; Teixeira, V.H.; Baptista, A.M.; Machuqueiro, M.. "Constant-pH MD Simulations of DMPA/DMPC Lipid Bilayers". Journal of Chemical Theory and Computation 11 12 (2015): 5973-5979. http://www.scopus.com/inward/record.url?eid=2-s2.0-84949633293&partnerID=MN8TOARS.
    10.1021/acs.jctc.5b00956
  18. Carvalheda, C.A.; Campos, S.R.R.; Baptista, A.M.. "The Effect of Membrane Environment on Surfactant Protein C Stability Studied by Constant-pH Molecular Dynamics". Journal of Chemical Information and Modeling 55 10 (2015): 2206-2217. http://www.scopus.com/inward/record.url?eid=2-s2.0-84945581645&partnerID=MN8TOARS.
    10.1021/acs.jcim.5b00076
  19. Correia, M.; Snabe, T.; Thiagarajan, V.; Petersen, S.B.; Campos, S.R.R.; Baptista, A.M.; Neves-Petersen, M.T.. "Photonic activation of plasminogen induced by low dose UVB". PLoS ONE 10 1 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84922108038&partnerID=MN8TOARS.
    10.1371/journal.pone.0116737
  20. Carvalheda, C.A.; Campos, S.R.R.; Machuqueiro, M.; Baptista, A.M.. "Correction to "structural effects of pH and deacylation on surfactant protein C in an organic solvent mixture: A constant-pH MD study"". Journal of Chemical Information and Modeling 55 1 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84921826482&partnerID=MN8TOARS.
    10.1021/ci5007454
  21. Vila-Viçosa, D.; Teixeira, V.H.; Baptista, A.M.; Machuqueiro, M.. "Constant-pH MD simulations of an oleic acid bilayer". Journal of Chemical Theory and Computation 11 5 (2015): 2367-2376. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929155290&partnerID=MN8TOARS.
    10.1021/acs.jctc.5b00095
  22. Magalhães, P.R.; Machuqueiro, M.; Baptista, A.M.. "Constant-pH molecular dynamics study of kyotorphin in an explicit bilayer". Biophysical Journal 108 9 (2015): 2282-2290. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929660265&partnerID=MN8TOARS.
    10.1016/j.bpj.2015.03.052
  23. Vila-Vic¸osa, D.; Teixeira, V.H.; Santos, H.A.F.; Baptista, A.M.; Machuqueiro, M.. "Treatment of ionic strength in biomolecular simulations of charged lipid bilayers". Journal of Chemical Theory and Computation 10 12 (2014): 5483-5492. http://www.scopus.com/inward/record.url?eid=2-s2.0-84916241903&partnerID=MN8TOARS.
    10.1021/ct500680q
  24. De Barros, D.P.C.; Campos, S.R.R.; Madeira, P.P.; Azevedo, A.M.; Baptista, A.M.; Aires-Barros, M.R.. "Modeling the partitioning of amino acids in aqueous two phase systems". Journal of Chromatography A 1329 (2014): 52-60. http://www.scopus.com/inward/record.url?eid=2-s2.0-84895141345&partnerID=MN8TOARS.
    10.1016/j.chroma.2013.12.015
  25. Oliveira, A.S.F.; Damas, J.M.; Baptista, A.M.; Soares, C.M.. "Exploring O2Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site". PLoS Computational Biology 10 12 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84919667074&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1004010
  26. Damas, J.M.; Baptista, A.M.; Soares, C.M.. "The pathway for O2 diffusion inside CotA laccase and possible implications on the multicopper oxidases family". Journal of Chemical Theory and Computation 10 8 (2014): 3525-3531. http://www.scopus.com/inward/record.url?eid=2-s2.0-84906245108&partnerID=MN8TOARS.
    10.1021/ct500196e
  27. Teixeira, V.H.; Vila-Viccosa, D.; Baptista, A.M.; Machuqueiro, M.. "Protonation of DMPC in a bilayer environment using a linear response approximation". Journal of Chemical Theory and Computation 10 5 (2014): 2176-2184. http://www.scopus.com/inward/record.url?eid=2-s2.0-84900529268&partnerID=MN8TOARS.
    10.1021/ct5000082
  28. Damas, J.M.; Filipe, L.C.S.; Campos, S.R.R.; Lousa, D.; Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Predicting the thermodynamics and kinetics of helix formation in a cyclic peptide model". Journal of Chemical Theory and Computation 9 11 (2013): 5148-5157. http://www.scopus.com/inward/record.url?eid=2-s2.0-84887835236&partnerID=MN8TOARS.
    10.1021/ct400529k
  29. Filipe, L.C.S.; Machuqueiro, M.; Darbre, T.; Baptista, A.M.. "Unraveling the conformational determinants of peptide dendrimers using molecular dynamics simulations". Macromolecules 46 23 (2013): 9427-9436. http://www.scopus.com/inward/record.url?eid=2-s2.0-84890366302&partnerID=MN8TOARS.
    10.1021/ma401574b
  30. Carvalheda, C.A.; Campos, S.R.R.; Machuqueiro, M.; Baptista, A.M.. "Structural effects of ph and deacylation on surfactant protein c in an organic solvent mixture: A constant-pH MD study". Journal of Chemical Information and Modeling 53 11 (2013): 2979-2989. http://www.scopus.com/inward/record.url?eid=2-s2.0-84888621173&partnerID=MN8TOARS.
    10.1021/ci400479c
  31. Lousa, D.; Baptista, A.M.; Soares, C.M.. "A molecular perspective on nonaqueous biocatalysis: Contributions from simulation studies". Physical Chemistry Chemical Physics 15 33 (2013): 13723-13736. http://www.scopus.com/inward/record.url?eid=2-s2.0-84881248110&partnerID=MN8TOARS.
    10.1039/c3cp51761f
  32. Filipe, L.C.S.; MacHuqueiro, M.; Baptista, A.M.. "Erratum: Unfolding the conformational behavior of peptide dendrimers: Insights from molecular dynamics simulations (Journal of the American Chemical Society (2011) 133 (5042-5052) DOI: 10.1021/ja111001v)". Journal of the American Chemical Society 134 49 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84870946509&partnerID=MN8TOARS.
    10.1021/ja311198h
  33. Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Structural determinants for the membrane insertion of the transmembrane peptide of hemagglutinin from influenza virus". Journal of Chemical Information and Modeling 52 11 (2012): 3001-3012. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870015416&partnerID=MN8TOARS.
    10.1021/ci3003396
  34. Soares, C.M.; Baptista, A.M.. "Simulation of multihaem cytochromes". FEBS Letters 586 5 (2012): 510-518. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857916893&partnerID=MN8TOARS.
    10.1016/j.febslet.2011.10.019
  35. Mateus, P.; Delgado, R.; Groves, P.; Campos, S.R.R.; Baptista, A.M.; Brandão, P.; Félix, V.. "Water encapsulation in a polyoxapolyaza macrobicyclic compound". Journal of Organic Chemistry 77 16 (2012): 6816-6824. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865230787&partnerID=MN8TOARS.
    10.1021/jo300799s
  36. Lousa, D.; Baptista, A.M.; Soares, C.M.. "Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using molecular dynamics simulations". Journal of Chemical Information and Modeling 52 2 (2012): 465-473. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857583770&partnerID=MN8TOARS.
    10.1021/ci200455z
  37. Vila-Viçosa, D.; Campos, S.R.R.; Baptista, A.M.; MacHuqueiro, M.. "Reversibility of prion misfolding: Insights from constant-PH molecular dynamics simulations". Journal of Physical Chemistry B 116 30 (2012): 8812-8821. http://www.scopus.com/inward/record.url?eid=2-s2.0-84864755277&partnerID=MN8TOARS.
    10.1021/jp3034837
  38. Lousa, D.; Cianci, M.; Helliwell, J.R.; Halling, P.J.; Baptista, A.M.; Soares, C.M.. "Interaction of counterions with subtilisin in acetonitrile: Insights from molecular dynamics simulations". Journal of Physical Chemistry B 116 20 (2012): 5838-5848. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862279541&partnerID=MN8TOARS.
    10.1021/jp303008g
  39. Filipe, L.C.S.; MacHuqueiro, M.; Baptista, A.M.. "Unfolding the conformational behavior of peptide dendrimers: Insights from molecular dynamics simulations". Journal of the American Chemical Society 133 13 (2011): 5042-5052. http://www.scopus.com/inward/record.url?eid=2-s2.0-79953908369&partnerID=MN8TOARS.
    10.1021/ja111001v
  40. Alexov, E.; Mehler, E.L.; Baker, N.; M. Baptista, A.; Huang, Y.; Milletti, F.; Erik Nielsen, J.; et al. "Progress in the prediction of pK a values in proteins". Proteins: Structure, Function and Bioinformatics 79 12 (2011): 3260-3275. http://www.scopus.com/inward/record.url?eid=2-s2.0-81055157643&partnerID=MN8TOARS.
    10.1002/prot.23189
  41. Machuqueiro, M.; Baptista, A.M.. "Is the prediction of pK a values by constant-pH molecular dynamics being hindered by inherited problems?". Proteins: Structure, Function and Bioinformatics 79 12 (2011): 3437-3447. http://www.scopus.com/inward/record.url?eid=2-s2.0-81055140448&partnerID=MN8TOARS.
    10.1002/prot.23115
  42. Lousa, D.; Baptista, A.M.; Soares, C.M.. "Structural determinants of ligand imprinting: A molecular dynamics simulation study of subtilisin in aqueous and apolar solvents". Protein Science 20 2 (2011): 379-386. http://www.scopus.com/inward/record.url?eid=2-s2.0-79251557782&partnerID=MN8TOARS.
    10.1002/pro.569
  43. Damas, J.M.; Oliveira, A.S.F.; Baptista, A.M.; Soares, C.M.. "Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: Molecular dynamics studies of HlyB". Protein Science 20 7 (2011): 1220-1230. http://www.scopus.com/inward/record.url?eid=2-s2.0-79959352522&partnerID=MN8TOARS.
    10.1002/pro.650
  44. Oliveira, A.S.F.; Baptista, A.M.; Soares, C.M.. "Inter-domain communication mechanisms in an ABC importer: A molecular dynamics study of the MalFGK 2E complex". PLoS Computational Biology 7 8 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80052311546&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1002128
  45. Oliveira, A.S.; Baptista, A.M.; Soares, C.M.. "Conformational changes induced by ATP-hydrolysis in an ABC transporter: A molecular dynamics study of the Sav1866 exporter". Proteins: Structure, Function and Bioinformatics 79 6 (2011): 1977-1990. http://www.scopus.com/inward/record.url?eid=2-s2.0-79955741987&partnerID=MN8TOARS.
    10.1002/prot.23023
  46. Campos, S.R.R.; Baptista, A.M.. "Erratum: Conformational analysis in a multidimensional energy landscape: Study of an arginylglutamate repeat (Journal of Physical Chemistry B (2009) 113 (15989))". Journal of Physical Chemistry B 114 23 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77953449669&partnerID=MN8TOARS.
    10.1021/jp103633j
  47. Campos, S.R.R.; MacHuqueiro, M.; Baptista, A.M.. "Constant-pH molecular dynamics simulations reveal a ß-rich form of the human prion protein". Journal of Physical Chemistry B 114 39 (2010): 12692-12700. http://www.scopus.com/inward/record.url?eid=2-s2.0-77957317648&partnerID=MN8TOARS.
    10.1021/jp104753t
  48. MacHuqueiro, M.; Campos, S.R.R.; Soares, C.M.; Baptista, A.M.. "Membrane-induced conformational changes of kyotorphin revealed by molecular dynamics simulations". Journal of Physical Chemistry B 114 35 (2010): 11659-11667. http://www.scopus.com/inward/record.url?eid=2-s2.0-77956326420&partnerID=MN8TOARS.
    10.1021/jp104418g
  49. Oliveira, A.S.F.; Baptista, A.M.; Soares, C.M.. "Insights into the molecular mechanism of an ABC transporter: Conformational changes in the NBD dimer of mj0796". Journal of Physical Chemistry B 114 16 (2010): 5486-5496. http://www.scopus.com/inward/record.url?eid=2-s2.0-77951539821&partnerID=MN8TOARS.
    10.1021/jp905735y
  50. Machuqueiro, M.; Baptista, A.M.. "Molecular dynamics at constant pH and reduction potential: Application to cytochrome c3". Journal of the American Chemical Society 131 35 (2009): 12586-12594. http://www.scopus.com/inward/record.url?eid=2-s2.0-69849094447&partnerID=MN8TOARS.
    10.1021/ja808463e
  51. Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin: Oxygen oxidoreductase from Desulfovibrio gigas". Journal of Biological Inorganic Chemistry 14 6 (2009): 853-862. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349289240&partnerID=MN8TOARS.
    10.1007/s00775-009-0497-5
  52. Campos, S.R.R.; Baptista, A.M.. "Conformational analysis in a multidimensional energy landscape: Study of an arginylglutamate repeat". Journal of Physical Chemistry B 113 49 (2009): 15989-16001. http://www.scopus.com/inward/record.url?eid=2-s2.0-71549167017&partnerID=MN8TOARS.
    10.1021/jp902991u
  53. Veríssimo, A.F.; Sousa, F.L.; Baptista, A.M.; Teixeira, M.; Pereira, M.M.. "Thermodynamic redox behavior of the heme centers in A-type heme-copper oxygen reductases: Comparison between the two subfamilies". Biophysical Journal 95 9 (2008): 4448-4455. http://www.scopus.com/inward/record.url?eid=2-s2.0-58149144256&partnerID=MN8TOARS.
    10.1529/biophysj.108.139493
  54. Sousa, F.L.; Veríssimo, A.F.; Baptista, A.M.; Soulimane, T.; Teixeira, M.; Pereira, M.M.. "Redox properties of Thermus thermophilus ba3: Different electron-proton coupling in oxygen reductases? (Biophysical Journal (2008) 94, (2434-2441)". Biophysical Journal 95 1 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-61349111548&partnerID=MN8TOARS.
    10.1529/biophysj.108.0900181
  55. Veríssimo, A.F.; Sousa, F.L.; Baptista, A.M.; Teixeira, M.; Pereira, M.M.. "Thermodynamic redox behavior of the heme centers of cbb3 heme-copper oxygen reductase from Bradyrhizobium japonicum (Biochemistry (2007) 46, 46, (13245-13253))". Biochemistry 47 19 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-43249129717&partnerID=MN8TOARS.
    10.1021/bi8005829
  56. Eberini, I.; Rocco, A.G.; Ientile, A.R.; Baptista, A.M.; Gianazza, E.; Tomaselli, S.; Molinari, H.; Ragona, L.. "Conformational and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein". Proteins: Structure, Function and Genetics 71 4 (2008): 1889-1898. http://www.scopus.com/inward/record.url?eid=2-s2.0-44349108965&partnerID=MN8TOARS.
    10.1002/prot.21875
  57. Rocco, A.G.; Mollica, L.; Ricchiuto, P.; Baptista, A.M.; Gianazza, E.; Eberini, I.. "Characterization of the protein unfolding processes induced by urea and temperature". Biophysical Journal 94 6 (2008): 2241-2251. http://www.scopus.com/inward/record.url?eid=2-s2.0-44049099949&partnerID=MN8TOARS.
    10.1529/biophysj.107.115535
  58. Sousa, F.L.; Veríssimo, A.F.; Baptista, A.M.; Soulimane, T.; Teixeira, M.; Pereira, M.M.. "Redox properties of thermus thermophilus ba3: Different electron-proton coupling in oxygen reductases?". Biophysical Journal 94 6 (2008): 2434-2441. http://www.scopus.com/inward/record.url?eid=2-s2.0-44049088504&partnerID=MN8TOARS.
    10.1529/biophysj.107.122614
  59. Teixeira, V.H.; Soares, C.M.; Baptista, A.M.. "Proton pathways in a [NiFe]-hydrogenase: A theoretical study". Proteins: Structure, Function and Genetics 70 3 (2008): 1010-1022. http://www.scopus.com/inward/record.url?eid=2-s2.0-38549139111&partnerID=MN8TOARS.
    10.1002/prot.21588
  60. Machuqueiro, M.; Baptista, A.M.. "Acidic range titration of HEWL using a constant-pH molecular dynamics method". Proteins: Structure, Function and Genetics 72 1 (2008): 289-298. http://www.scopus.com/inward/record.url?eid=2-s2.0-44949173075&partnerID=MN8TOARS.
    10.1002/prot.21923
  61. Machuqueiro, M.; Baptista, A.M.. "The pH-dependent conformational states of kyotorphin: A constant-pH molecular dynamics study". Biophysical Journal 92 6 (2007): 1836-1845. http://www.scopus.com/inward/record.url?eid=2-s2.0-33947640091&partnerID=MN8TOARS.
    10.1529/biophysj.106.092445
  62. Gaspar, P.; Neves, A.R.; Shearman, C.A.; Gasson, M.J.; Baptista, A.M.; Turner, D.L.; Soares, C.M.; Santos, H.. "The lactate dehydrogenases encoded by the ldh and ldhB genes in Lactococcus lactis exhibit distinct regulation and catalytic properties - Comparative modeling to probe the molecular basis". FEBS Journal 274 22 (2007): 5924-5936. http://www.scopus.com/inward/record.url?eid=2-s2.0-35748951589&partnerID=MN8TOARS.
    10.1111/j.1742-4658.2007.06115.x
  63. Veríssimo, A.F.; Sousa, F.L.; Baptista, A.M.; Teixeira, M.; Pereira, M.M.. "Thermodynamic redox behavior of the heme centers of cbb3 heme-copper oxygen reductase from Bradyrhizobium japonicum". Biochemistry 46 46 (2007): 13245-13253. http://www.scopus.com/inward/record.url?eid=2-s2.0-36348983845&partnerID=MN8TOARS.
    10.1021/bi700733g
  64. Rocha, R.; Leal, S.S.; Teixeira, V.H.; Regalla, M.; Huber, H.; Baptista, A.M.; Soares, C.M.; Gomes, C.M.. "Natural domain design: Enhanced thermal stability of a zinc-lacking ferredoxin isoform shows that a hydrophobic core efficiently replaces the structural metal site". Biochemistry 45 34 (2006): 10376-10384. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748694511&partnerID=MN8TOARS.
    10.1021/bi0610698
  65. Machuqueiro, M.; Baptista, A.M.. "Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling in decalysine". Journal of Physical Chemistry B 110 6 (2006): 2927-2933. http://www.scopus.com/inward/record.url?eid=2-s2.0-33644745556&partnerID=MN8TOARS.
    10.1021/jp056456q
  66. Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Pathways of H2 toward the active site of [NiFe]-hydrogenase". Biophysical Journal 91 6 (2006): 2035-2045. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748456960&partnerID=MN8TOARS.
    10.1529/biophysj.106.084376
  67. Micaelo, N.M.; Baptists, A.M.; Soares, C.M.. "Parametrization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic liquid for the GROMOS force field". Journal of Physical Chemistry B 110 29 (2006): 14444-14451. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746915678&partnerID=MN8TOARS.
    10.1021/jp061869s
  68. Lopes, S.C.D.N.; Soares, C.M.; Baptista, A.M.; Goormaghtigh, E.; Cabral, B.J.C.; Castanho, M.A.R.B.. "Conformational and orientational guidance of the analgesic dipeptide kyotorphin induced by lipidic membranes: Putative correlation toward receptor docking". Journal of Physical Chemistry B 110 7 (2006): 3385-3394. http://www.scopus.com/inward/record.url?eid=2-s2.0-33644895138&partnerID=MN8TOARS.
    10.1021/jp053651w
  69. Oliveira, A.S.F.; Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Reorganization and conformational changes in the reduction of tetraheme cytochromes". Biophysical Journal 89 6 (2005): 3919-3930. http://www.scopus.com/inward/record.url?eid=2-s2.0-28444483273&partnerID=MN8TOARS.
    10.1529/biophysj.105.065144
  70. Teixeira, V.H.; Cunha, C.A.; Machuqueiro, M.; Oliveira, A.S.F.; Victor, B.L.; Soares, C.M.; Baptista, A.M.. "On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium". Journal of Physical Chemistry B 109 30 (2005): 14691-14706. http://www.scopus.com/inward/record.url?eid=2-s2.0-23844500381&partnerID=MN8TOARS.
    10.1021/jp052259f
  71. Micaelo, N.M.; Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Water dependent properties of cutinase in nonaqueous solvents: A computational study of enantioselectivity". Biophysical Journal 89 2 (2005): 999-1008. http://www.scopus.com/inward/record.url?eid=2-s2.0-23244449490&partnerID=MN8TOARS.
    10.1529/biophysj.105.063297
  72. Rivas, L.; Soares, C.M.; Baptista, A.M.; Simaan, J.; Di Paolo, R.E.; Murgida, D.H.; Hildebrandt, P.. "Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: Surface-enhanced resonance raman spectroscopy and simulation studies". Biophysical Journal 88 6 (2005): 4188-4199. http://www.scopus.com/inward/record.url?eid=2-s2.0-22244481835&partnerID=MN8TOARS.
    10.1529/biophysj.104.057232
  73. Eberini, I.; Baptista, A.M.; Gianazza, E.; Fraternali, F.; Beringhelli, T.. "Reorganization in Apo- and Holo-ß-Lactoglobulin Upon Protonation of Glu89: Molecular Dynamics and pKa Calculations". Proteins: Structure, Function and Genetics 54 4 (2004): 744-758. http://www.scopus.com/inward/record.url?eid=2-s2.0-1542316338&partnerID=MN8TOARS.
    10.1002/prot.10643
  74. Bento, I.; Matias, P.M.; Baptista, A.M.; Da Costa, P.N.; Van Dongen, W.M.A.M.; Saraiva, L.M.; Schneider, T.R.; Soares, C.M.; Carrondo, M.A.. "Molecular Basis for Redox-Bohr and Cooperative Effects in Cytochrome c 3 from Desulfovibrio desulfuricans ATCC 27774: Crystallographic and Modeling Studies of Oxidized and Reduced High-Resolution Structures at pH 7.6". Proteins: Structure, Function and Genetics 54 1 (2004): 135-152. http://www.scopus.com/inward/record.url?eid=2-s2.0-0348047621&partnerID=MN8TOARS.
    10.1002/prot.10431
  75. Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Theoretical identification of proton channels in the quinol oxidase aa 3 from Acidianus ambivalens". Biophysical Journal 87 6 (2004): 4316-4325. http://www.scopus.com/inward/record.url?eid=2-s2.0-10044240740&partnerID=MN8TOARS.
    10.1529/biophysj.104.049353
  76. Soares, C.M.; Baptista, A.M.; Pereira, M.M.; Teixeira, M.. "Investigation of protonatable residues in Rhodothermus marinus caa 3 haem-copper oxygen reductase: Comparism with Paracoccus denitrificans aa3 haem-copper oxygen reductase". Journal of Biological Inorganic Chemistry 9 2 (2004): 124-134. http://www.scopus.com/inward/record.url?eid=2-s2.0-1542298196&partnerID=MN8TOARS.
    10.1007/s00775-003-0509-9
  77. Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Modeling Electron Transfer Thermodynamics in Protein Complexes: Interaction between Two Cytochromes c3". Biophysical Journal 86 5 (2004): 2773-2785. http://www.scopus.com/inward/record.url?eid=2-s2.0-2142644598&partnerID=MN8TOARS.
    10.1016/S0006-3495(04)74331-3
  78. Bento, I.; Teixeira, V.H.; Baptista, A.M.; Soares, C.M.; Matias, P.M.; Carrondo, M.A.. "Redox-Bohr and other cooperativity effects in the nine-heme cytochrome c from Desulfovibrio desulfuricans ATCC 27774: Crystallographic and modeling studies". Journal of Biological Chemistry 278 38 (2003): 36455-36469. http://www.scopus.com/inward/record.url?eid=2-s2.0-0141815636&partnerID=MN8TOARS.
    10.1074/jbc.M301745200
  79. Soares, C.M.; Teixeira, V.H.; Baptista, A.M.. "Protein structure and dynamics in nonaqueous solvents: Insights from molecular dynamics simulation studies". Biophysical Journal 84 3 (2003): 1628-1641. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037342275&partnerID=MN8TOARS.
  80. Teixeira, V.H.; Soares, C.M.; Baptista, A.M.. "Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail". Journal of Biological Inorganic Chemistry 7 1-2 (2002): 200-216. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036359052&partnerID=MN8TOARS.
    10.1007/s007750100287
  81. Baptista, A.M.; Teixeira, V.H.; Soares, C.M.. "Constant-pH molecular dynamics using stochastic titration". Journal of Chemical Physics 117 9 (2002): 4184-4200. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036732086&partnerID=MN8TOARS.
    10.1063/1.1497164
  82. Baptista, A.M.. "Comment on "explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines" [J. Chem. Phys. 114, 9706 (2001)]". Journal of Chemical Physics 116 17 (2002): 7766-7768. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036573188&partnerID=MN8TOARS.
    10.1063/1.1465399
  83. Louro, R.O.; Bento, I.; Matias, P.M.; Catarino, T.; Baptista, A.M.; Soares, C.M.; Carrondo, M.A.; Turner, D.L.; Xavier, A.V.. "Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome". Journal of Biological Chemistry 276 47 (2001): 44044-44051. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035941269&partnerID=MN8TOARS.
    10.1074/jbc.M107136200
  84. Mendes, J.; Baptista, A.M.; Carrondo, M.A.; Soares, C.M.. "Implicit solvation in the self-consistent mean field theory method: Sidechain modelling and prediction of folding free energies of protein mutants". Journal of Computer-Aided Molecular Design 15 8 (2001): 721-740. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034748018&partnerID=MN8TOARS.
    10.1023/A:1012279810260
  85. Baptista, A.M.; Scares, C.M.. "Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins". Journal of Physical Chemistry B 105 1 (2001): 293-309. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035120969&partnerID=MN8TOARS.
  86. Mendes, J.; Baptista, A.M.; Carrondo, M.A.; Soares, C.M.. "Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model". Proteins: Structure, Function and Genetics 37 4 (1999): 530-543. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032732306&partnerID=MN8TOARS.
    10.1002/(SICI)1097-0134(19991201)37:4<530::AID-PROT4>3.0.CO;2-H
  87. Martel, P.J.; Soares, C.M.; Baptista, A.M.; Fuxreiter, M.; Náray-Szabó, G.; Louro, R.O.; Carrondo, M.A.. "Comparative redox and pK(a) calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods". Journal of Biological Inorganic Chemistry 4 1 (1999): 73-86. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032588946&partnerID=MN8TOARS.
    10.1007/s007750050291
  88. Baptista, A.M.; Martel, P.J.; Soares, C.M.. "Simulation of electron-proton coupling with a Monte Carlo method: Application to cytochrome c3 using continuum electrostatics". Biophysical Journal 76 6 (1999): 2978-2998. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033001692&partnerID=MN8TOARS.
    10.1016/S0006-3495(99)77452-7
  89. Baptista, A.M.; Jonson, P.H.; Hough, E.; Petersen, S.B.. "The origin of trypsin: Evidence for multiple gene duplications in trypsins". Journal of Molecular Evolution 47 3 (1998): 353-362. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031718943&partnerID=MN8TOARS.
    10.1007/PL00006393
  90. Baptista, A.M.; Martel, P.J.; Petersen, S.B.. "Simulation of protein conformational freedom as a function of pH: Constant-pH molecular dynamics using implicit titration". Proteins: Structure, Function and Genetics 27 4 (1997): 523-544. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030970305&partnerID=MN8TOARS.
    10.1002/(SICI)1097-0134(199704)27:4<523::AID-PROT6>3.0.CO;2-B
  91. Sebastião, M.J.; Martel, P.; Baptista, A.; Petersen, S.B.; Cabral, J.M.S.; Aires-Barros, M.R.. "Predicting the partition coefficients of a recombinant cutinase in polyethylene glycol/phosphate aqueous two-phase systems". Biotechnology and Bioengineering 56 3 (1997): 248-257. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031555165&partnerID=MN8TOARS.
    10.1002/(SICI)1097-0290(19971105)56:3<248::AID-BIT2>3.0.CO;2-J
  92. Jones, R.A.; Haraldseth, O.; Baptista, A.M.; Müller, T.B.; Øksendal, A.N.. "A study of the contribution of changes in the cerebral blood volume to the haemodynamic response to anoxia in rat brain". NMR in Biomedicine 10 2 (1997): 59-66. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030749195&partnerID=MN8TOARS.
    10.1002/(SICI)1099-1492(199704)10:2<59::AID-NBM415>3.0.CO;2-0
  93. Jones, R.A.; Haraldseth, O.; Baptista, A.M.; Müller, T.B.; Øksendal, A.N.. "A study of the contribution of changes in the cerebral blood volume to the haemodynamic response to anoxia in rat brain". NMR in Biomedicine 9 6 (1996): 233-240. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030235961&partnerID=MN8TOARS.
  94. Jones, R.A.; Müller, T.B.; Haraldseth, O.; Baptista, A.M.; Øksendal, A.N.. "Cerebrovascular changes in rats during ischemia and reperfusion: A comparison of BOLD and first pass bolus tracking techniques". Magnetic Resonance in Medicine 35 4 (1996): 489-496. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029879652&partnerID=MN8TOARS.
  95. Anthonsen, H.W.; Baptista, A.; Drabløs, F.; Martel, P.; Petersen, S.B.; Sebastião, M.; Vaz, L.. "Lipases and esterases: a review of their sequences, structure and evolution.". Biotechnology annual review 1 (1995): 315-371. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029418050&partnerID=MN8TOARS.
    10.1016/S1387-2656(08)70056-5
  96. Anthonsen, H.W.; Baptista, A.; Drabløs, F.; Martel, P.; Petersen, S.B.. "The blind watchmaker and rational protein engineering". Journal of Biotechnology 36 3 (1994): 185-220. http://www.scopus.com/inward/record.url?eid=2-s2.0-0028031316&partnerID=MN8TOARS.
    10.1016/0168-1656(94)90152-X
  97. Pires, M.J.; Martel, P.; Baptista, A.; Petersen, S.B.; Willson, R.C.; Cabral, J.M.S.. "Improving protein extraction yield in reversed micellar systems through surface charge engineering". Biotechnology and Bioengineering 44 7 (1994): 773-780. http://www.scopus.com/inward/record.url?eid=2-s2.0-0028501097&partnerID=MN8TOARS.
Livro
  1. Lousa, D.; Baptista, A.M.; Soares, C.M.. Hydration effects on enzyme properties in nonaqueous media analyzed by MD simulations. 2016.
    10.4032/9789814669337
  2. Martel, P.J.; Baptista, A.; Petersen, S.B.. Protein Electrostatics. 1996.
    10.1016/S1387-2656(08)70016-4
  3. Baptista, A.; Brautaset, T.; Drabløs, F.; Martel, P.; Valla, S.; Petersen, S.B.. Electrostatic studies of carbohydrate active enzymes. 1995.
    10.1016/S0921-0423(06)80103-6
Poster em conferência
  1. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "pH gradients in continuum electrostatics calculations of Ccox". Trabalho apresentado em EJIBCE 2014 (2nd Encontro de Jovens Investigadores de Biologia Estrutural Computacional), Coimbra, Portugal, 2014.
  2. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Continuum electrostatics calculations of Ccox in the presence of a pH gradient". Trabalho apresentado em Protein Electrostatics Satellite Meeting of EBEC 2014, Lisboa, Portugal, 2014.
  3. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Titration of key sites in bacteriorhodopsin in the presence of a pH gradient". Trabalho apresentado em Frontiers in dynamics simulations of biological molecules, Barcelona, Spain, 2013.
  4. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Probing energy transduction mechanisms in bacteriorhodopsin using electrostatic calculations". Trabalho apresentado em EBSA 2013 (9th European Biophysics Congress), Lisboa, Portugal, 2013.
  5. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Continuum electrostatics study of energy transduction mechanisms in bacteriorhodopsin". Trabalho apresentado em COST Action CM0902 Training School on Molecular machineries for ion translocation across membranes, Lisboa, Portugal, 2013.
  6. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "The effect of pH on the interaction between the neuropeptide kyotorphin and a lipid bilayer: a molecular simulation study". Trabalho apresentado em X Girona Seminar on Theoretical and Computational Chemistry for the Modeling of Biochemical Systems: From Theory to Applications, Girona, Spain, 2012.
  7. Baptista, António M.; Magalhães, Pedro R.; Campos, Sara R. R.; Machuqueiro, Miguel. "Ionization of a neuropeptide unaffected by the membrane environment: simulations of kyotorphin using constant-pH MD and linear response approximation". Trabalho apresentado em Gordon Research Conference on Protons & Membrane Reactions, San Francisco, USA, 2012.
  8. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Simulation of explicit bilayers with constant-pH molecular dynamics". Trabalho apresentado em 5th Theoretical Biophysics International Symposium, Madeira, Portugal, 2011.
  9. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Constant-pH molecular dynamics simulations of the neuropeptide kyotorphin in a lipid bilayer". Trabalho apresentado em Frontiers in Protein Research Interbio Symposium, Oeiras, Portugal, 2011.
  10. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Constant-pH molecular dynamics simulations of explicit membranes: study of peptide-bilayer interactions". Trabalho apresentado em V Spanish-Portuguese Biophysics Congress, Zaragoza, Spain, 2010.
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2023/06/27 How does pH affect the distribution of ions around proteins? Protein Electrostatics Conference
Istituto Italiano di Tecnologia (Genova, Itália)
2021/05/05 How to address the effect of pH on protein dimerization: a constant-pH MD study of beta-lactoglobulin Protein Electrostatics Conference
Istituto Italiano di Tecnologia (Genova, Itália)
2021/03/02 Constant-pH molecular simulations using stochastic titration: Illustration with peptide dendrimers. Simulation of Open Systems In Chemistry, Pharma, Food Science, and Immuno-Diagnostics: Rare-Event Methods At Constant Chemical Potentials Including Constant pH
CECAM-IRL (Dublin, Irlanda)
2018/06/26 Electrostatics of peptide dendrimers: standard MD and constant-pH MD Protein Electrostatics 2018
University of Belgrade (Belgrade, Sérvia)
2017/06/26 Electrostatics of peptide dendrimers: standard MD and constant-pH MD Workshop on Protein Electrostatics
Telluride Science Research Center (Telluride CO, Estados Unidos)
2016/07/21 Constant-pH MD of cytochrome c oxidase Proteins Electrostatics Berlin 2016
Freie Universität Berlin (Berlin, Alemanha)
2015/08/19 Constant-pH molecular dynamics simulations of membrane systems: titrable lipids and proton pumps 250th American Chemical Society National Meeting
American Chemical Society (Boston MA, Estados Unidos)
2015/08/18 Including acid-base equilibrium in computer simulations using constant-pH molecular dynamics 250th American Chemical Society National Meeting
American Chemical Society (Boston MA, Estados Unidos)
2015/07/08 Constant-pH MD of cytochrome c oxidase Workshop on Protein Electrostatics
Telluride Science Research Center (Telluride CO, Estados Unidos)
2014/07/10 Constant-pH MD in membrane environments: from mimetic solvents, to peptide internalization, to pH gradients Protein Electrostatics - Satellite Meeting of EBEC 2014
University of Lisbon (Lisbon, Portugal)
2013/07/10 Constant-pH molecular dynamics in membrane environments: two unexpected results Workshop on Protein Electrostatics
Telluride Science Research Center (Telluride CO, Estados Unidos)
2012/08/22 Inherited problems of the stochastic titration method for constant-pH MD 244th American Chemical Society National Meeting
American Chemical Society National (Philadelphia PA, Estados Unidos)
2012/07/01 Constant-pH molecular dynamics using stochastic titration: theory and applications The 9th AIMS Conference on Dynamical Systems, Differential Equations and Applications
American Institute of Mathematical Sciences (Orlando FL, Estados Unidos)
2011/07/14 Some inherited problems of constant-pH molecular dynamics Workshop on Protein Electrostatics
Telluride Science Research Center (Telluride CO, Estados Unidos)
2010/08/03 Constant-pH molecular dynamics: achievements, problems and open questions Workshop on Proton Transfer in Biology
Telluride Science Research Center (Telluride CO, Estados Unidos)
2009/09/15 Molecular dynamics simulations at constant pH and reduction potential Cofactor-Protein Interactions in Biological Processes
Freie Universität Berlin (Berlin, Alemanha)
2009/07/08 Conformation-protonation coupling: the counter-intuitive case of succinic acid Workshop on Protein Electrostatics
Telluride Science Research Center (Telluride CO, Estados Unidos)
2008/07/16 Molecular dynamics simulations at constant pH and reduction potential Workshop on Protein Electrostatics
Telluride Science Research Center (Telluride CO, Estados Unidos)
Distinções

Outra distinção

2013 FCT Investigator (ref. IF/01713/2013)
Fundação para a Ciência e a Tecnologia, Portugal
2001 Post-doctoral fellowship (ref. BPD/5740/2001)
Fundação para a Ciência e a Tecnologia, Portugal
1998 Post-doctoral fellowship (ref. BPD/18899/98)
Fundação para a Ciência e a Tecnologia, Portugal
1997 Research fellowship (ref. BIC/1921/97)
Fundação para a Ciência e a Tecnologia, Portugal
1994 PhD fellowship (ref. BD/3749/94)
Fundação para a Ciência e a Tecnologia, Portugal
1991 PhD fellowship (ref. BD/1338/91-IF)
Fundação para a Ciência e a Tecnologia, Portugal