Professor auxiliar
Faculdade de Ciências e Tecnologia
Subsistema
Docentes Universitário
Unidade ID externa
Centro de Investigação em Tecnologias e Serviços de Saúde (CINTESIS)
Regime
Exclusividade
Vínculo
CT em Funções Públicas por tempo indeterminado
Paulo J. Martel graduated in Biochemistry from the Faculty of Sciences at the University of Lisbon in 1988 and went on to earn a PhD in Protein Electrostatics from the Instituto de Tecnologia Química e Biológica (ITQB, Universidade Nova de Lisboa) in 1996. His doctoral research, carried out in collaboration with Novo Nordisk A/S in Denmark and the MR-Senteret at SINTEF in Norway, focused on the computational modeling of electrostatic interactions in proteins—a field that has remained central to his career.
From 1993 to 1996, he continued at ITQB as a postdoctoral researcher, working on molecular modeling of bacterial redox proteins. In 1999, he joined the University of Algarve (Campus de Gambelas), where he has since served as Assistant Professor of Biochemistry, Bioinformatics, and Computational Drug Design. He is also a Principal Investigator at the Centro de Investigação em Tecnologias e Serviços de Saúde (CINTESIS-RISE). Between 2004 and 2014, he coordinated the Centre for Molecular and Structural Biomedicine (CBME), overseeing its research strategy and scientific development.
Martel leads the Biomolecular Simulation Laboratory, a group dedicated to developing and applying advanced computational methods for protein simulation. His team designs high-performance computing approaches in C and Python, optimized for both CPU and GPU architectures, and applies them to pH-dependent molecular dynamics, electrostatic and protonation modeling, docking, and molecular dynamics simulations. These methods have been used to explore a wide range of biological systems, from cytochromes P450 and bacterial redox proteins to endoplasmic reticulum chaperones and the FOXO family of transcription factors.
Beyond his research, he has contributed to scientific policy and evaluation in Portugal, having served as a member of the Scientific Committee for the SCML Neuroscience Prizes, as a grant evaluator for the Agência de Inovação (ANI) in the fields of Bioinformatics and Computational Biology, and currently as an invited expert for the Portuguese Agency for Assessment and Accreditation of Higher Education (A3ES).
His expertise spans protein electrostatics, constant-pH molecular dynamics, structural bioinformatics, protein–ligand interactions, and high-performance scientific computing, with recent interests also extending into machine learning applications in structural biology.
Atividades
Atividades
2018 - Presente. Outro júri / avaliação. Member of evaluation panel for Agência Nacional de Informação (ANI) research grants.. Agência Nacional de Inovação SA.
2016/11/01 - Presente. Orientação. Interacção entre isotiocianatos e citocromos P450: um estudo de docking computacional.Mestrado (Mestrado). Orientador.
2014/09/22 - Presente. Curso / Disciplina lecionado. Molecular modelling and Computational Drug Design. Ciências Farmacêuticas (Mestrado integrado). Universidade do Algarve.
2013 - Presente. Membro de comissão. Member of the Scientific Committee for Neurosciences Scientific Prizes of Santa Casa da Misericórdia de Lisboa. Duties including evaluatio of grant progress reports and counselling an all issues related with prize regulations and management of applications. . Consultor. Santa Casa da Misericórdia de Lisboa.
2013 - Presente. Curso / Disciplina lecionado. Computational Biology. Ciências Biomédicas (Mestrado integrado). Universidade do Algarve.
2004/10/01 - Presente. Curso / Disciplina lecionado. Bioinformática. Bioquímica. Universidade do Algarve.
2004/02/01 - Presente. Curso / Disciplina lecionado. Bioquímica Estrutural. Bioquímica (Licenciatura). Universidade do Algarve.
1999/03/01 - Presente. Curso / Disciplina lecionado. Enzymology. Bioquímica (Licenciatura). Universidade do Algarve.
2025/06/23 - 2035/06/26. Participação em evento. International conference Protein Electrostatics, June 23-26, 2025, Lisbon, Portugal. Conferência. Protein Electrostatics 2025. Fundação da Faculdade de Ciências da Universidade de Lisboa.
2026/07/05 - 2026/07/10. Arbitragem científica em conferência. 49th International Congress of Theoretical Chemists of Latin Expression . CIBB -- Universidade de Coimbra.
2024/01/24 - 2024/01/25. Participação em evento. Running GROMACS molecular modelling software on the LUMI supercomputer.. Oficina (workshop). Running GROMACS efficiently on LUMI workshop 2024. EuroHPC Joint Undertaking.
2024/07/29 - 2024/07/31. Participação em evento. Workshop meeting for the project "VirusHostAi: a range of computational approaches" . Encontro. "VIRUSHOSTAI: A Range of Computational Approaches. Universidade de Coimbra Centro de Inovação em Biomedicina e Biotecnologia.
2024/07/29. Apresentação oral de trabalho. A conformation-dependent redox relayat the core ofprotein disulphide isomerase (PDI)activity. "VIRUSHOSTAI: A Range of Computational Approaches. CIBB -- Universidade de Coimbra (Figueira da Foz, Portugal).
2023/12/06 - 2023/12/09. Participação em evento. EMBO Workshop: Computational structural biology. Conferência. EMBO Workshop: Computational structural biology. European Molecular Biology Laboratory.
2023/07/03. Júri de grau académico. Bis-ureias derivadas de benzo[b]tiofeno para a inibição de agregados Aß-LilrB2 na Doença de Alzheimer: uma investigação in silico. Arguente principal. Joel José Pereira Santos (Mestrado). Universidade de Aveiro.
2023/05/16. Júri de grau académico. A new generation of user-friendly and machine learning-accelerated methods for protein pKa calculations. Arguente principal. Pedro de Brito Pires Santos Reis (Doutoramento). Fundação da Faculdade de Ciências da Universidade de Lisboa.
2023/04/14. Júri de grau académico. Interacções proteína-proteína e proteína-RNA na proteína não-estrutural 1 (NS1) do vírus Influenza. Arguente principal. Nícia Filipa Rosário Ferreira (Doutoramento). Universidade de Coimbra.
2020/03 - 2022/12/15. Orientação. Descoberta de moléculas moduladoras da interação Foxo3-DNA.Ciências Farmacêuticas (Mestrado). Orientador.
2022/10/10 - 2022/10/13. Organização de evento. 11th IBERGRID Iberian Grid Computation Conference (2022). Infraestrutura Nacional de Computação Distribuída; Universidade do Algarve; Consejo Superior de Investigaciones Científicas; Laboratório de Instrumentação e Física Experimental de Partículas.
2021/11/02 - 2021/11/04. Participação em evento. 3D-BioInfo 2021 Annual Meeting: Structural bioinformatics . Conferência. 3D-BioInfo 2021 Annual Meeting. ELIXIR, Wellcome Genome Campus.
2021/05/04 - 2021/05/05. Participação em evento. PDB50: A special symposium celebrating the 50th anniversary of the Protein Data Bank . Conferência. PDB50: A special symposium celebrating the 50th anniversary of the Protein Data Bank. World Wide Protein Databank.
2010 - 2015. Orientação. Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems.Computational Biochemisry (Doutoramento). Orientador.
2004. Apresentação oral de trabalho. Evolutionary relationship between bone and matrix Gla proteins. . XIV Congresso Nacional de Bioquímica,. Sociedade Portuguesa de Bioquímica (Vilamoura, Portugal).
Projetos
Projetos
2023/03 - 2033/09. Search for molecular modulators of Foxo3a activity.
2025/01/01 - 2027/12/31. expressCDx - Identification of RNA Biomarkers for the Development of New Personalized Cancer Diagnostic Methods. Investigador responsável. Universidade do Algarve.
2026/01 - 2027/06. SenDrug: Cell-Type-Specific Drug Repurposing for Targeting Senescence..
2024 - 2024. Implementation of a Constant-pH Molecular Dynamics Simulation Protocol for proteins and its application to the study of the binding of the SARS-CoV-2 S S-protein to the ACE2 human protein receptor.
2023/03/01 - 2023/09/30. Search for molecular modulators of Foxo3a activity, Projetos de Computação Avançada. Investigador responsável. Universidade do Algarve - Campus de Gambelas; Centro de Investigação em Tecnologias e Serviços de Saúde.
2016/05 - 2019/10. Regeneracao no Ratinho Espinoso Africano.
2012/02 - 2015/10. Alternative splicing and its impact on molecular networks during stem cell differentiation.
2012/02 - 2015/04. A Biophysical Approach to Oxidative Protein Folding in the ER: Relative Importance of Ero1 and Prdx4 alternative pathways.
2011/01/01 - 2012/12/31. Projecto Estratégico - LA 23 - 2011-2012, 6817 - DCRRNI ID. Universidade do Algarve; Fundação da Faculdade de Ciências da Universidade de Lisboa; Instituto de Biotecnologia e Bioengenharia; Universidade do Minho; Universidade de Trás-os-Montes e Alto Douro; Fundação Gaspar Frutuoso; Universidade de Lisboa Instituto Superior Técnico; Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento; Universidade dos Açores.
2009/01/01 - 2012/12/31. Caracterização Termodinâmica da Activação do Receptor de Pregnanos PXR através da Técnica da Microbalança de Cristal de Quartzo com Calorimetria de Condução de Calor, 3599-PPCDT. Universidade do Algarve; Universidade do Algarve Faculdade de Ciências e Tecnologia.
2009/01 - 2012/12. Thermodynamic Signature of the Pregnane Xenobiotic Receptor Activation by Quartz Crystal Microbalance with Heat Conduction Calorimetry.
2009/01 - 2012/06. Biomolecular Engineering Approches for in vitro Production of Self Assembly Viral Nanoparticles.
2005/04/01 - 2008/06/30. Estudos Teóricos e Experimentais sobre Conformação, Energética e Dinâmica Enzimática do Citocromo CYP3A4, POCI. Universidade do Algarve; Universidade do Algarve Faculdade de Ciências e Tecnologia.
2005/04 - 2008/06. Theoretical and Experimental Studies of Enzyme Conformation, Energetics and Dynamics of CYP3A4.
2003 - 2005. Relationship between CYP3A4 gene polymorphisms, protein structure and activity in disease setting.
2002 - 2004. Structure and function of elicitins and their role in the infection of the cork oak by Phytophthora cinnamomi.
2001 - 2003. Molecular modelling of bacterial redox proteins: methodology and applications.
2000 - 2002. Structure-function relationships of serine hydrolases in non-conventional solvents.
1996 - 1998. Molecular modelling of electron-transfer proteins.
Produções
Maia-Fernandes, A.C.; Pais de Azevedo, T.; Borralho-Martins, Nísia; Ramalhete, S.; Martins, G.G.; Palmeirim, I.; Duarte, I.; et al. 2026. "A Morphometric Characterization Of Early Chick Embryo Elongation". Developmental Biology, 531: 19-29. https://doi.org/10.1016/j.ydbio.2025.12.022
Melo EP; Soukaina El-Guendouz; Cátia Correia; Fernando Teodoro; Carlos Lopes; Paulo J. Martel. 2024. "A Conformational-Dependent Interdomain Redox Relay at the Core of Protein Disulfide Isomerase Activity". Antioxidants & Redox Signaling, 41: 181-200. https://doi.org/10.1089/ars.2023.0288
Filoemena Nascimento; Gonçalo Braga; Paulo J. Martel. 2024. "Identification of Small-Molecule Modulators of FOXO3 Through Virtual Screening". Em FOXO Transcription Factors: Methods and Protocols, 115-128. 1stª ed. Springer. https://doi.org/10.1007/978-1-0716-4217-7_11
Muhammad Shoaib Malik; Paulo Martel. 2024. Using Positional Embedding and Transformer-Based Siamese Neural Network to Predict Genetic Homologues for Future Protein Structure Prediction. https://doi.org/10.2139/ssrn.4952228
Santos, Bruno F.; Grenho, Inês; Martel, Paulo; Ferreira, Bibiana I.; Link, Wolfgang. Autor correspondente: Link, Wolfgang. 2023. "FOXO family isoforms". Cell Death & Disease, 14 (10). https://doi.org/10.1038/s41419-023-06177-1
Zhi, Xiangyun; Vieira, Ana; Huse, Kristin K.; Martel, Paulo; Lobkowicz, Ludmila; Li, Ho Kwong; Croucher, Nick; et al. Autor correspondente: Sriskandan, Shiranee. 2023. "Characterization of the RofA regulon in the pandemic M1global and emergent M1UK lineages of Streptococcus pyogenes". Microbial Genomics, 9 (12). https://doi.org/10.1099/mgen.0.001159
Duarte, ARB; Magno, Ramiro; Martel, Paulo; Ghezzo, Marinella; Xavier, Joana M; Maia, Ana-Teresa. 2020. Exploring the role of alternative splicing in breast cancer risk. Em CANCER BIOLOGY: FROM BASIC TO TRANSLATIONAL RESEARCH.
Martins, A.M.; Latham, J.A.; Martel, P.J.; Barr, I.; Iavarone, A.T.; Klinman, J.P.. 2019. "A two-component protease in Methylorubrum extorquens with high activity toward the peptide precursor of the redox cofactor pyrroloquinoline quinone". Journal of Biological Chemistry, 294 (41): 15025-15036. https://doi.org/10.1074/jbc.RA119.009684
Martel, Paulo; Gouveia, Patrícia. 2017. "Player Experience, Gaming and Virtual Reality Technologies.". Revista de Ciências da Computação, 12: 25-43.
Marques CL; Fernández I; Viegas MN; Cox CJ; Martel P; Rosa J; Cancela ML; et al. 2015. "Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives.". Cellular and Molecular Life Sciences, 73 (4): 841-857. https://doi.org/10.1007/s00018-015-2024-x
Varanda CM; Machado M; Martel P; Nolasco G; Clara MI; Félix MR. 2015. "Correction: Genetic Diversity of the Coat Protein of Olive Mild Mosaic Virus (OMMV) and Tobacco Necrosis Virus D (TNV-D) Isolates and Its Structural Implications.". https://doi.org/10.1371/journal.pone.0128171
Silva G; Lima FP; Martel P; Castilho R. 2014. "Thermal adaptation and clinal mitochondrial DNA variation of European anchovy.". Proceedings of the Royal Society B: Biological Sciences, 281 (1792). https://doi.org/10.1098/rspb.2014.1093
Varanda CM; Machado M; Martel P; Nolasco G; Clara MI; Félix MR. 2014. "Genetic diversity of the coat protein of Olive mild mosaic virus (OMMV) and Tobacco necrosis virus D (TNV-D) isolates and its structural implications.". PLoS One, 9 (10). https://doi.org/10.1371/journal.pone.0110941
Freedman, Holly; Martel, Paulo; Cruzeiro, Leonor. 2011. "Mixed quantum-classical dynamics of an amide-I vibrational excitation in a protein alpha-helix (vol 82, 174308, 2010)". Physical Review B, 84 (13). https://doi.org/10.1103/PhysRevB.84.139902
Freedman, Holly; Martel, Paulo; Cruzeiro, Leonor. 2011. "Erratum: Mixed quantum-classical dynamics of an amide-I vibrational excitation in a protein a-helix [Phys. Rev. B 82, 174308 (2010)]". https://doi.org/10.1103/PhysRevB.84.139902
Teixeira VH; Ribeiro V; Martel PJ. 2010. "Analysis of binding modes of ligands to multiple conformations of CYP3A4.". Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1804 (10): 2036-2045. https://doi.org/10.1016/j.bbapap.2010.06.008
Tiago T; Martel P; Gutiérrez-Merino C; Aureliano M. 2007. "Binding modes of decavanadate to myosin and inhibition of the actomyosin ATPase activity.". Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1774 (4): 474-480. https://doi.org/10.1016/j.bbapap.2007.02.004
Rodrigues ML; Archer M; Martel P; Miranda S; Thomaz M; Enguita FJ; Baptista RP; et al. 2006. "Crystal structures of the free and sterol-bound forms of beta-cinnamomin.". Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1764 (1): 110-121. https://doi.org/10.1016/j.bbapap.2005.09.008
Laizé V; Martel P; Viegas CS; Price PA; Cancela ML. 2005. "Evolution of matrix and bone gamma-carboxyglutamic acid proteins in vertebrates.". Journal of Biological Chemistry, 280 (29): 26659-26668. https://doi.org/10.1074/jbc.M500257200
Laizé, Vincent; Martel, Paulo; Viegas, Carla S. B.; Cancela, M. Leonor. 2005. "Conserved features of matrix and bone gamma-carboxyglutamic acid proteins in vertebrates - an evolutionary point of view". Trabalho apresentado em 2nd joint meeting of ECTS and IBMS, June 25-29, Geneva, Switzerland. https://doi.org/10.1016/j.bone.2005.04.001
Martel, Paulo. 2005. "Docking studies of ligands to cytochrome P450: evaluation and optimization of the Autodock automated docking procedure, P Martel, D Rodrigues, G Ferreira, V Marques, 14th Int. Conf. on Cytochromes P450, Dallas, Texas, USA, May 31 – June 5.". Trabalho apresentado em 14th Int. Conf. on Cytochromes P450, Dallas, Texas, USA, May 31 – June 5., Dallas, Estados Unidos.
Rodrigues ML; Archer M; Martel P; Jacquet A; Cravador A; Carrondo MA. 2002. "Structure of beta-cinnamomin, a protein toxic to some plant species.". Biological Crystallography, 58 (8): 1314-1321. https://doi.org/10.1107/S0907444902010107
Martel, P. J.; Rodrigues, L.; Cravador, A.. 2002. "Electrostatic calculations on fungal elicitins". Abstracts of Papers of the American Chemical Society, 223: C72-C72. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000176296801804&KeyUID=WOS:000176296801804
Baptista AM; Martel PJ; Soares CM. 1999. "Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics.". Biophysical Journal, 76 (6): 2978-2998. https://doi.org/10.1016/S0006-3495(99)77452-7
Martel PJ; Soares CM; Baptista AM; Fuxreiter M; Náray-Szabó G; Louro RO; Carrondo MA. 1999. "Comparative redox and pKa calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods.". Journal of Biological Inorganic Chemistry, 4 (1): 73-86. https://doi.org/10.1007/s007750050291
Soares CM; Martel PJ; Mendes J; Carrondo MA. 1998. "Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations.". Biophysical journal, 74(4), 1708-1721., 74 (4): 1708-1721. https://doi.org/10.1016/S0006-3495(98)77882-8
Sebastião MJ; Martel P; Baptista A; Petersen SB; Cabral JM; Aires-Barros MR. 1997. "Predicting the partition coefficients of a recombinant cutinase in polyethylene glycol/phosphate aqueous two-phase systems.". Biotechnology and bioengineering, 56 (3): 248-257. https://doi.org/10.1002/(SICI)1097-0290(19971105)56:3<248::AID-BIT2>3.0.CO;2-J
Soares, C. M.; Martel, P. J.; Carrondo, M. A.. 1997. "Theoretical studies on the redox-Bohr effect in cytochrome c(3) from Desulfovibrio vulgaris Hildenborough". Journal of Biological Inorganic Chemistry, 2 (6): 714-727. https://doi.org/10.1007/s007750050188
Petersen MT; Martel P; Petersen EI; Drabløs F; Petersen SB. 1997. "Surface and electrostatics of cutinases.". Methods in enzymology (Vol. 284, pp. 130-154), 284: 130-154. https://doi.org/10.1016/S0076-6879(97)84009-8
Baptista, A.M.; Martel, P.J.; Petersen, S.B.; Baptista AM; Martel PJ; Petersen SB. 1997. "Simulation of protein conformational freedom as a function of pH: Constant-pH molecular dynamics using implicit titration". Proteins: Structure, Function and Genetics, 27 (4): 523-544. https://doi.org/10.1002/(SICI)1097-0134(199704)27:4<523::AID-PROT6>3.0.CO;2-B
Martel, Paulo J.; Baptista, António; Petersen, Steffen B.. 1996. "Protein Electrostatics". Em Biotechnology Annual Review, 315-372. Vol. 2. Estados Unidos: Elsevier. https://doi.org/10.1016/s1387-2656(08)70016-4
Anthonsen, Henrik W.; Baptista, António; Drabløs, Finn; Martel, Paulo; Petersen, Steffen B.; Sebastião, Maria; Vaz, Louis. 1995. "Lipases and esterases: a review of their sequences, structure and evolution". Em Biotechnology Annual Review Volume 1, 315-371. Vol. 1. Elsevier. https://doi.org/10.1016/s1387-2656(08)70056-5
Baptista, Antonio; Brautaset, Trygve; Drabløs, Finn; Martel, Paulo; Valla, Svein; Petersen, Steffen B.. 1995. "Electrostatic studies of carbohydrate active enzymes". Em Carbohydrate Bioengineering, Proceedings of an International Conference, editado por Petersen, S. B.; Svensson, B.; Pedersen, S., 181-204. Elsevier. https://doi.org/10.1016/s0921-0423(06)80103-6
Baptista, A.; Brautaset, T.; Drablos, F.; Martel, P.; Valla, S.; Petersen, S. B.. 1995. "Electrostatic studies of carbohydrate active enzymes". Editado por Petersen, S. B.; Svensson, B.; Pedersen, S., 181-204. Vol. 10. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:A1995BE87L00015&KeyUID=WOS:A1995BE87L00015
Martel, Paulo. 1994. "Protein Engineering". Suiça.
Anthonsen, Henrik W.; Baptista, António; Drabløs, Finn; Martel, Paulo; Petersen, Steffen B.. 1994. "The blind watchmaker and rational protein engineering". Journal of Biotechnology, 36 (3): 185-220. https://doi.org/10.1016/0168-1656(94)90152-x
Pires MJ; Martel P; Baptista A; Petersen SB; Willson RC; Cabral JM. 1994. "Improving protein extraction yield in reversed micellar systems through surface charge engineering.". Biotechnology and bioengineering, 44 (7): 773-780. https://doi.org/10.1002/bit.260440702
Martel, Paulo; Petersen, S.B.. 1991. "Electrostatics of proteins". Em Site-Directed Mutagenesis and Protein Engineering: Proceedings of the International Symposium on Site-Directed Mutagenesis and Protein Engineering, editado por El-Geweli, M.R, 31-36. 1stª ed. Estados Unidos: Elsevier Science Ltd.