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Identification

Personal identification

Full name
António José Meireles Ribeiro

Citation names

  • Ribeiro, António
  • António J. M. Ribeiro

Author identifiers

Ciência ID
471D-534E-682F
ORCID iD
0000-0002-2533-1231

Email addresses

  • antonio.ribeiro@fc.up.pt (Professional)

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Chemical Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Proficiency (C2) Advanced (C1) Proficiency (C2) Advanced (C1)
Italian Elementary (A2) Elementary (A2) Beginner (A1) Elementary (A2) Beginner (A1)
Education
Degree Classification
2019/12/31
Concluded
 Master of Science In Finance (Master)
The Open University Business School, United Kingdom
"Valuation and Outcomes of Mergers and Acquisitions in the Pharmaceutical and Biotechnology Sector" (THESIS/DISSERTATION)
 Distinction
2013/09/07
Concluded
 Química Sustentável (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Università della Calabria, Italy
"Drug design targeted at HIV-1 Integrase" (THESIS/DISSERTATION)
2009/09/29
Concluded
 Bioquímica (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
"Quantum mechanics study of the hydrolysis of phosphodiester bonds" (THESIS/DISSERTATION)
 18
2008/02/20
Concluded
 Bioquímica (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal
 16
Affiliation

Science

Category
Host institution 		Employer
2023/07/01 - Current Researcher (Research) REQUIMTE LAQV Porto, Portugal
Universidade do Porto Departamento de Química e Bioquímica, Portugal
(...)
2016/06/01 - 2021/12/31 Postdoc (Research) European Bioinformatics Institute, United Kingdom
European Bioinformatics Institute, United Kingdom
2014/01/01 - 2016/05/31 Postdoc (Research) Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
Universidade do Porto Faculdade de Ciências, Portugal
2014/01 - 2014/03 Visiting Researcher (Research) Universidade do Porto Faculdade de Ciências, Portugal
Nanyang Technological University, Singapore
2011/02 - 2012/02 Visiting Researcher (Research) Universidade do Porto Faculdade de Ciências, Portugal
Università della Calabria, Italy

Teaching in Higher Education

Category
Host institution 		Employer
2024/02 - 2024/08 Invited Assistant Professor (University Teacher) Universidade do Porto Faculdade de Ciências, Portugal
Universidade do Porto Faculdade de Ciências, Portugal

Others

Category
Host institution 		Employer
2022/01/01 - 2023/06/30 Bioinformatics Consultant European Bioinformatics Institute, United Kingdom
Projects

Grant

Designation Funders
2023/07/01 - 2029/06/30 "Catalytic Predictor": An Automated Computational Tool to Characterise Enzyme Reaction Mechanisms
2022.03058.CEECIND
Principal investigator
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2014 - 2016 The effect of enzyme flexibility on the catalytic mechanism of HIV-1 Protease
SFRH/BPD/94883/2013
Post-doc Fellow
Fundação para a Ciência e a Tecnologia
2013 - 2013 ENZYMATIC CATALYSIS - seeking a global picture
EXCL/QEQ-COM/0394/2012
Research Fellow
Universidade do Porto Faculdade de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2009 - 2013 Drug Design Targeted At HIV-1 Integrase
SFRH/BD/61549/2009
PhD Student Fellow
Fundação para a Ciência e a Tecnologia
2008 - 2009 Design de novos Fármacos dirigidos ao virus HIV-1
FCT PTDC/QUI/68302/2006
Research Fellow
Universidade do Porto Faculdade de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia

Contract

Designation Funders
2019/01/01 - 2019/12/31 Unidade de Ciências Biomoleculares Aplicadas
UID/Multi/04378/2019
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2011/01/01 - 2012/12/31 Strategic Project - LA 6 - 2011-2012
PEst-C/EQB/LA0006/2011
Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Conference poster
  1. "Survey of the Enzyme Catalytic Residues in Mechanism and Catalytic Site Atlas". Paper presented in EMBL-EBI Research Retreat - 2019, 2019.
  2. "A Survey of Enzyme Chemistry". Paper presented in Encontro de Jovens Investigadores de Biologia Computacional Estrutural - 2018, 2018.
  3. "Identifying pseudoenzymes using the Mechanism and Catalytic Site Atlas (M-CSA)". Paper presented in Pseudoenzymes 2018: From molecular mechanisms to cell biology, Sardinia, Italy., 2018.
  4. "M-CSA Mechanism And Catalytic Site Atlas: A Database of Enzyme Mechanisms". Paper presented in EMBL Conference: Revolutions in Structural Biology: Celebrating the 100th Anniversary of Sir John Kendrew, Heidelberg, Germany, 2017.
  5. "Redesign and Update of MACiE". Paper presented in EMBL Postdoc Retreat 2017, Alsace, France, 2017.
  6. "Redesign of MACiE: A database of enzyme mechanisms". Paper presented in American Chemical Society Fall 2017 - Chemistry's Impact on the Global Economy, Washington DC, USA., 2017.
  7. "Evaluation of DFT Functionals in the Context of the Hydrolysis of Phosphodiester Bonds". Paper presented in THEOBio 2011 - 5Th Theoretical Biophysics International Symposium, 2011.
Journal article
  1. Ioannis G. Riziotis; Jenny C. Kafas; Gabriel Ong; Neera Borkakoti; António J. M. Ribeiro; Janet M. Thornton. "Paradigms of convergent evolution in enzymes". The FEBS Journal (2024): https://doi.org/10.1111/febs.17332.
    10.1111/febs.17332
  2. Antonio J. M. Ribeiro; Ioannis G. Riziotis; Neera Borkakoti; Janet M. Thornton. "Enzyme function and evolution through the lens of bioinformatics". Biochemical Journal (2023): https://doi.org/10.1042/BCJ20220405.
    10.1042/BCJ20220405
  3. Antonio J. M. Ribeiro; Ioannis G. Riziotis; Jonathan D. Tyzack; Neera Borkakoti; Janet M. Thornton. "EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions". Nature Methods (2023): https://doi.org/10.1038/s41592-023-02006-7.
    10.1038/s41592-023-02006-7
  4. Ioannis G. Riziotis; António J.M. Ribeiro; Nivedita Borkakoti; Janet M Thornton. "The 3D Modules of Enzyme Catalysis: Deconstructing Active Sites into Distinct Functional Entities". Journal of Molecular Biology (2023): http://dx.doi.org/10.1016/j.jmb.2023.168254.
    10.1016/j.jmb.2023.168254
  5. António J. M. Ribeiro; Ioannis G. Riziotis; Jonathan D. Tyzack; Neera Borkakoti; Janet M. Thornton. "Using mechanism similarity to understand enzyme evolution". Biophysical Reviews (2022): https://doi.org/10.1007/s12551-022-01022-9.
    10.1007/s12551-022-01022-9
  6. Charles A Santana; Sandro C Izidoro; Raquel C de Melo-Minardi; Jonathan D Tyzack; António J M Ribeiro; Douglas E V Pires; Janet M Thornton; Sabrina de A. Silveira. "GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs". Nucleic Acids Research (2022): https://doi.org/10.1093/nar/gkac323.
    10.1093/nar/gkac323
  7. Rossana Zaru; Joseph Onwubiko; Antonio J. M. Ribeiro; Keeva Cochrane; Jonathan D. Tyzack; Venkatesh Muthukrishnan; Lukas Pravda; et al. "The Enzyme Portal: an integrative tool for enzyme information and analysis". The FEBS Journal (2021): https://doi.org/10.1111/febs.16168.
    10.1111/febs.16168
  8. Antonio J. M. Ribeiro; Jonathan D. Tyzack; Neera Borkakoti; Janet M. Thornton. "Identifying pseudoenzymes using functional annotation: pitfalls of common practice". The FEBS Journal 287 19 (2020): 4128-4140. https://doi.org/10.1111/febs.15142.
    10.1111/febs.15142
  9. António J.M. Ribeiro; Jonathan D. Tyzack; Neera Borkakoti; Gemma L. Holliday; Janet M. Thornton. "A global analysis of function and conservation of catalytic residues in enzymes". Journal of Biological Chemistry 295 2 (2020): 314-324. https://doi.org/10.1074/jbc.REV119.006289.
    10.1074/jbc.REV119.006289
  10. "PDBe-KB: a community-driven resource for structural and functional annotations". Nucleic Acids Research 48 D1 (2020): D344-D353.
    10.1093/nar/gkz853
  11. "GRaSP: a graph-based residue neighborhood strategy to predict binding sites". Bioinformatics 36 Supplement (2020): i726-i734.
    10.1093/bioinformatics/btaa805
  12. Tyzack JD; Ribeiro AJM; Borkakoti N; Thornton JM. "Exploring Chemical Biosynthetic Design Space with Transform-MinER.". ACS synthetic biology (2019): http://europepmc.org/abstract/med/31647630.
    10.1021/acssynbio.9b00105
  13. António J. M. Ribeiro; Sayoni Das; Natalie Dawson; Rossana Zaru; Sandra Orchard; Janet M. Thornton; Christine Orengo; et al. "Emerging concepts in pseudoenzyme classification, evolution, and signaling". Science Signaling 12 594 (2019): https://doi.org/10.1126/scisignal.aat9797.
    10.1126/scisignal.aat9797
  14. Tyzack JD; Ribeiro AJM; Borkakoti N; Thornton JM. "Transform-MinER: transforming molecules in enzyme reactions.". Bioinformatics (Oxford, England) (2018): http://europepmc.org/abstract/med/29762650.
    10.1093/bioinformatics/bty394
  15. Tyzack JD; Fernando L; Ribeiro AJM; Borkakoti N; Thornton JM. "Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.". Structure (London, England : 1993) (2018): http://europepmc.org/abstract/med/29551288.
    10.1016/j.str.2018.02.009
  16. António J M Ribeiro; Gemma L Holliday; Nicholas Furnham; Jonathan D Tyzack; Katherine Ferris; Janet M Thornton. "Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites". Nucleic Acids Research (2018): https://doi.org/10.1093/nar/gkx1012.
    10.1093/nar/gkx1012
  17. Martin-Herranz DE; Ribeiro AJM; Krueger F; Thornton JM; Reik W; Stubbs TM. "cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.". Nucleic acids research (2017): http://europepmc.org/abstract/med/29036576.
    10.1093/nar/gkx814
  18. Hu Z; Sim Y; Kon OL; Ng WH; Ribeiro AJ; Ramos MJ; Fernandes PA; et al. "Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy.". Bioconjugate chemistry (2017): http://europepmc.org/abstract/med/28049291.
    10.1021/acs.bioconjchem.6b00682
  19. Pereira, Andreia T.; Ribeiro, António J. M.; Fernandes, Pedro A.; Ramos, Maria J.. "Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases". International Journal of Quantum Chemistry (2017): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000406687800002&KeyUID=WOS:000406687800002.
    10.1002/qua.25409
  20. Oliveira EF; Santos-Martins D; Ribeiro AM; Brás NF; Cerqueira NS; Sousa SF; Ramos MJ; Fernandes PA. "HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015).". Expert opinion on therapeutic patents (2016): http://europepmc.org/abstract/med/27537201.
    10.1080/13543776.2016.1216977
  21. Sousa, S.F.; Ribeiro, A.J.M.; Neves, R.P.P.; Brás, N.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms". Wiley Interdisciplinary Reviews: Computational Molecular Science (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84984706224&partnerID=MN8TOARS.
    10.1002/wcms.1281
  22. Barra, P.A.; Ribeiro, A.J.M.; Ramos, M.J.; Jiménez, V.A.; Alderete, J.B.; Fernandes, P.A.. "Binding free energy calculations on E-selectin complexes with sLex oligosaccharide analogs". Chemical Biology and Drug Design (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84988310710&partnerID=MN8TOARS.
    10.1111/cbdd.12837
  23. Sousa, S.F.; Sousa, J.F.M.; Barbosa, A.C.C.; Ferreira, C.E.; Neves, R.P.P.; Ribeiro, A.J.M.; Fernandes, P.A.; Ramos, M.J.. "Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)". Journal of Physical Chemistry A 120 27 (2016): 5300-5306. http://www.scopus.com/inward/record.url?eid=2-s2.0-84978708569&partnerID=MN8TOARS.
    10.1021/acs.jpca.6b01536
  24. Pinto, Gaspar P.; Ribeiro, Antonio J. M.; Ramos, Maria J.; Fernandes, Pedro A.; Toscano, Marirosa; Russo, Nino. "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
  25. Ribeiro, Antonio J. M.; Yang, Lifeng; Ramos, Maria J.; Fernandes, Pedro A.; Liang, Zhao-Xun; Hirao, Hajime. "Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase". Acs Catalysis 5 6 (2015): 3740-3751. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000355964300062&KeyUID=WOS:000355964300062.
    10.1021/acscatal.5b00528
  26. Shi, Yan X.; Liang, Rong Z.; Martin, Katherine A.; Weston, Nicholas; Gonzalez-Calera, Silvia; Ganguly, Rakesh; Li, Yongxin; et al. "Synthesis and Hydrolytic Studies on the Air-Stable [(4-CN-PhO)(E)P(mu-(NBu)-Bu-t)](2) (E = O, S, and Se) Cyclodiphosphazanes". Inorganic Chemistry 54 13 (2015): 6423-6432. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000357705800044&KeyUID=WOS:000357705800044.
    10.1021/acs.inorgchem.5b00735
  27. Ribeiro, Antonio J. M.; Santos-Martins, Diogo; Russo, Nino; Rarnos, Maria J.; Fernandes, Pedro A.. "Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease". Acs Catalysis 5 9 (2015): 5617-5626. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000361089700073&KeyUID=WOS:000361089700073.
    10.1021/acscatal.5b00759
  28. Araujo, Ana R.; Ribeiro, Antonio J. M.; Fernandes, Pedro A.; Ramos, Maria 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
  29. Hong, M.-K.; Ribeiro, A.J.M.; Kim, J.-K.; Ngo, H.-P.-T.; Kim, J.; Lee, C.H.; Ahn, Y.-J.; et al. "Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli". Acta Crystallographica Section D: Biological Crystallography 70 5 (2014): 1297-1310. http://www.scopus.com/inward/record.url?eid=2-s2.0-84900416783&partnerID=MN8TOARS.
    10.1107/S1399004714002570
  30. Brás, N.F.; Ribeiro, A.J.M.; Oliveira, M.; Paixão, N.M.; Tamames, J.A.; Fernandes, P.A.; Ramos, M.J.. "Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: Trends and patterns". Journal of Molecular Modeling 20 6 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84901542884&partnerID=MN8TOARS.
    10.1007/s00894-014-2271-z
  31. 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
  32. Sousa, S.F.; Pinto, G.R.P.; Ribeiro, A.J.M.; Coimbra, J.T.S.; Fernandes, P.A.; Ramos, M.J.. "Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes". Journal of Computational Chemistry 34 24 (2013): 2079-2090. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885957406&partnerID=MN8TOARS.
    10.1002/jcc.23349
  33. Sousa, S.F.; Ribeiro, A.J.M.; Coimbra, J.T.S.; Neves, R.P.P.; Martins, S.A.; Moorthy, N.S.H.N.; Fernandes, P.A.; Ramos, M.J.. "Protein-ligand docking in the new millennium - A retrospective of 10 years in the field". Current Medicinal Chemistry 20 18 (2013): 2296-2314. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877933286&partnerID=MN8TOARS.
    10.2174/0929867311320180002
  34. Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.; Russo, N.. "Erratum: A DFT study of the applicability of the charge balance model in two-metal enzymes: The case of cAMP-dependent protein kinase (Chemical Physics Letters (2012) 51:49 12242-12245)". Chemical Physics Letters 579 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84880331802&partnerID=MN8TOARS.
    10.1016/j.cplett.2013.06.024
  35. Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.; Russo, N.. "A DFT study of the applicability of the charge balance model in two-metal enzymes: The case of cAMP-dependent protein kinase". Chemical Physics Letters 571 (2013): 66-70. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877833562&partnerID=MN8TOARS.
    10.1016/j.cplett.2013.03.085
  36. 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
  37. Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.. "Benchmarking of DFT functionals for the hydrolysis of phosphodiester bonds". Journal of Chemical Theory and Computation 6 8 (2010): 2281-2292. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955561344&partnerID=MN8TOARS.
    10.1021/ct900649e
Preprint
  1. Ioannis G. Riziotis; António J. M. Ribeiro; Neera Borkakoti; Janet M. Thornton. "The 3D modules of enzyme catalysis: deconstructing active sites into distinct functional entities". 2023. https://doi.org/10.1101/2023.06.01.543252.
    10.1101/2023.06.01.543252
  2. Antonio J. M. Ribeiro; Ioannis G. Riziotis; Jonathan D. Tyzack; Neera Borkakoti; Janet M. Thornton. "EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions". 2022. https://doi.org/10.1101/2022.09.05.506575.
    10.1101/2022.09.05.506575
  3. Ioannis G. Riziotis; António J. M. Ribeiro; Neera Borkakoti; Janet M. Thornton. "Conformational variation in enzyme catalysis: A structural study on catalytic residues". 2021. https://doi.org/10.1101/2021.12.12.472283.
    10.1101/2021.12.12.472283
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/06/29 A Global Survey of Pseudoenzymes Across Evolutionary Families Pseudoenzyme functions across life - challenges and opportunities
EMBO (Girona, Spain)
2022/11/16 EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions EBI Industry Programme
EMBL-EBI (Cambridge, United Kingdom)
2022/10/05 Reporting Guidelines for Enzyme Reaction Mechanisms The 18th Strenda Meeting
Beilstein-Institut (Rudesheim, Germany)
2022/06/03 An Automated Tool To Propose Mechanisms of Enzyme Reactions Girona Seminar
(Spain)
2021/01/29 Enzyme Portal and the M-CSA - Two online resources from the EBI to explore data related to enzymes Standardization of Biocatalytic Reactions Webminar
University of Exeter (Remote, United Kingdom)
2018/07/11 Identifying PseudoEnzymes across protein families using M-CSA EMBL-EBI Research Retreat
EMBL-EBI (Essex, United Kingdom)
2017/12/22 Using the Mechanism and Catalytic Site Atlas (M-CSA) to understand enzyme function and evolution V Encontro de Jovens Investigadores de Biologia Computacional Estrutural
Universidade De Coimbra (Coimbra, Portugal)
2017/11/02 Using Mechanism and Catalytic Site Atlas to Understand Enzyme Function and Evolution EBI Research Talks
EMBL-EBI (Cambridge, United Kingdom)
2016/10/17 Redesigning MACiE - A Database of Enzymatic Mechanisms EBI Postdoc Day
EMBL-EBI (Cambridge, United Kingdom)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2025/02 - Current Finding new enzymes to degrade plastics
Co-supervisor
2023/09 - 2024/03 Rules of Enzyme Catalysis to Understand Enzyme Function and Evolution – A Quantum Mechanics study
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2020 - 2024 Analysis of the Catalytic Residues of Enzyme Active Sites
Co-supervisor of Ioannis Riziotis
European Bioinformatics Institute, United Kingdom
2020/06/01 - 2020/09/01 2020 Curation Internship for the Update of M-CSA (Mechanism and Catalytic Site Atlas)
Supervisor of Noa Marson
European Bioinformatics Institute, United Kingdom
2020/06/01 - 2020/09/01 2020 Curation Internship for the Update of M-CSA (Mechanism and Catalytic Site Atlas)
Supervisor of Yordanos Abeje
European Bioinformatics Institute, United Kingdom
2020/06/01 - 2020/09/01 2020 Curation Internship for the Update of M-CSA (Mechanism and Catalytic Site Atlas)
Supervisor of Trung Nguyen
European Bioinformatics Institute, United Kingdom
2020/06/01 - 2020/06/09 2020 Curation Internship for the Update of M-CSA (Mechanism and Catalytic Site Atlas)
Supervisor of Marko Babic
European Bioinformatics Institute, United Kingdom
2018/06 - 2018/09 2018 Curation Internship for the Update of M-CSA (Mechanism and Catalytic Site Atlas)
Supervisor of Amelia Brasnett
European Bioinformatics Institute, United Kingdom
2018/06 - 2018/09 2018 Curation Internship for the Update of M-CSA (Mechanism and Catalytic Site Atlas)
Supervisor of Charity Hornby
European Bioinformatics Institute, United Kingdom
2018/06 - 2018/09 2018 Curation Internship for the Update of M-CSA (Mechanism and Catalytic Site Atlas)
Supervisor of James Willey
European Bioinformatics Institute, United Kingdom
2018/06 - 2018/09 2018 Curation Internship for the Update of M-CSA (Mechanism and Catalytic Site Atlas)
Supervisor of Morwenna Hall
European Bioinformatics Institute, United Kingdom
2017/06 - 2017/11 Finding PseudoEnzymes related to enzymes in M-CSA
Supervisor of Jean O'Driscoll
European Bioinformatics Institute, United Kingdom
2017/06 - 2017/08 Creation of Videos of Enzyme Mechanisms
Supervisor of Souroprobho Chowdhury
European Bioinformatics Institute, United Kingdom
2016/07/04 - 2016/09 Revision of enzyme mechanism store in the MACiE database
Supervisor of Katherine Ferris
European Bioinformatics Institute, United Kingdom
2015 - 2016 Reaction Mechanism of the oxidation of DBT by DszB studied by QM/MM calculations
Co-supervisor of Cleide Ferreira
Universidade do Porto Faculdade de Ciências, Portugal
2013/03 - 2014/03 The catalytic mechanism of Retroviral Integrase for the strand transfer reaction explored by QM/MM calculations
Co-supervisor of Ana Rita Araújo
Universidade do Porto Faculdade de Ciências, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2016/09/20 - 2016/09/23 Participation in Course and Poster Presentation at the EMBL-EBI, Cambridge. Poster titled: Redesigning MACiE
Workshop
 Structural Bioinformatics Course
European Bioinformatics Institute, United Kingdom
2014/07/09 - 2014/07/11 Biochemical Assays for Screening Workshop
Workshop
European ScreeningPort GmbH, Hamburg, Germany, Germany
2014/05/19 - 2014/05/20 Participation in Workshop in London, United Kindgom.
Workshop
 Research Commercialization: From Ideas to IPO
Elsevier Ltd, United Kingdom
2009/08/15 - 2009/09/15 Participation in the Intensive Course of the European Master in Theoretical Chemistry and Computational Modelling in Groningen (Netherlands) and Leuven (Belgium)
Other
 4th edition of the Intensive Course of the European Master in Theoretical Chemistry and Computational Modelling (TCCM
Katholieke Universiteit Leuven, Belgium

Rijksuniversiteit Groningen, Netherlands

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2025/01/17 Enzymatic Synthesis of Rna-peptide Conjugates as Potential Therapeutics for Covid-19
(Thesis) Main arguer
 Ricardo Daniel González da Cunha (PhD)
Universidade de Coimbra Instituto de Investigação Interdisciplinar, Portugal
2024/07/25 Mecanismo de ação e desenvolvimento de antídotos para o veneno da víbora terciopelo (Mechanism of action and development of antidotes for the terciopelo viper venom)
(Thesis) Main arguer
 Marina Alexandra Ribeiro Moreira (Other)
Universidade do Porto Faculdade de Ciências, Portugal
2024/07/09 Understanding the Molecular Basis Behind Congenital Disorders of Glycosylation
(Thesis) Main arguer
 Pedro Afonso Eira Gonçalves (Other)
Instituto Politecnico do Porto Escola Superior de Tecnologia da Saúde do Porto, Portugal
2022/09/29 In Silico Approaches for the Detection of Zinc Ion in Regulatory Proteins
(Thesis) Main arguer
 Ulyana Motresku (Master)
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2024/10 - Current Molecular Biology and Evolution (1537-1719) Oxford Academic
2024/10 - 2024/10 Molecular Biology and Evolution (1537-1719) Oxford University Press
2024/09 - 2024/09 Scientific Reports (2045-2322) Nature Portfolio
2024/07 - 2024/07 Genomics, Proteomics & Bioinformatics (2210-3244) Oxford Academic
2023/09 - 2023/09 Protein Science (1469-896X) Wiley-Blackwell
2023/07 - 2023/07 Molecular Pharmaceuticals (1543-8384) American Chemical Society
2022/09 - 2022/09 Biochemical Society Transactions (1470-8752) Portland Press
2022/08 - 2022/08 Scientific Reports (2045-2322) Nature Portfolio
2022/03 - 2022/03 Journal of Chemical Information and Modelling (1520-5142) American Chemical Society
2021/06/01 - 2021/06/15 Topics in Catalyis Springer Nature

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2024/03 - Current Bioinformática Molecular (Molecular Bioinformatics) Bioinformática e Biologia Computacional (Mestrado integrado) Universidade do Porto Faculdade de Ciências, Portugal
2024/03 - Current Ómicas Funcionais (Functional Omics) Aplicações em Biotecnologia e Biologia Sintética (Mestrado integrado) Universidade do Porto Faculdade de Ciências, Portugal
2023/09 - Current Bioquímica Computacional (Computational Biochemistry) Bioquímica (Mestrado integrado) Universidade do Porto Faculdade de Ciências, Portugal
2023/08 - 2024/02 Modelação de Bioestruturas (Biostructures Modelling) Química (Licenciatura) Universidade do Porto Faculdade de Ciências, Portugal
2016/04/21 - 2016/04/21 Aula - Computational Chemistry and Enzymatic Catalysis Bioquímica (Licenciatura) Universidade do Porto Faculdade de Ciências, Portugal
2016/04/14 - 2016/04/14 Aula - Estudos de Docking com Integrase do HIV-1 e Screening Virtual Bioquímica (Licenciatura) Universidade do Porto Faculdade de Ciências, Portugal
2015/12/11 - 2015/12/11 Aula - Integração Termodinâmica ou Alquimia Computacional Bioquímica (Licenciatura) Universidade do Porto Faculdade de Ciências, Portugal
2015/07/16 - 2015/07/16 Workshop - Molecular Docking of Integrase Inhibitors with AutoDock Vina (Doutoramento) Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Mentoring / Tutoring

Topic Student name
2025/01 - Current Bioactive peptides for enzyme inhibition João Sousa

Other jury / evaluation

Activity description Institution / Organization
2021/05/22 - 2021/05/22 Avaliação do Projeto de Tese do Doutoramento de Ricardo Gonzalez (Final do Primeiro Ano de Doutoramento) sobre o desenvolvimento de enzimas para terapias com derivados sintéticos de RNA Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal