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João T. S. COIMBRA is an early-career researcher at the Associated Laboratory for Green Chemistry (LAQV, REQUIMTE). His research focuses on the molecular mechanisms underlying antimicrobial resistance (AMR), particularly how bacterial enzymes modify and degrade antibiotics. With a background in molecular and cellular biochemistry, he earned his Ph.D. in Sustainable Chemistry in 2017 from the Universities of Nova Lisbon and Porto, specializing in computational biochemistry. During his Ph.D., he worked on drug design, studying molecular transport through biological membranes and developing computational tools for studying protein-protein interactions. He also gained industry experience as a research consultant for PepsiCo, Inc. (USA). Afterward, he joined the Research Unit on Applied Molecular Biosciences (UCIBIO) as a postdoctoral fellow, focusing on drug development for type-II diabetes (project: NORTE-01-0145-FEDER-000024). In 2020, he secured a Recognized Researcher (R2) position through the highly competitive Individual Call of the Portuguese National Science Foundation (CEECIND, FCT), a role he currently holds (https://doi.org/10.54499/CEECIND/01374/2018/CP1545/CT0003). João collaborates across multiple scientific fields, including inorganic and organic chemistry, chemical synthesis, and membrane biophysics. He has built strong international partnerships with researchers in Europe, America, Asia, and Oceania. His expertise lies in computational methods applied to biomolecules, including molecular dynamics (MD) simulations, enhanced sampling techniques, hybrid quantum mechanics/molecular mechanics (QM/MM) methods, multi-resolution modeling, and structural bioinformatics. He authored 32 indexed publications, including highly prestigious journals, such as JACS Au, Chemical Science, and Journal of Molecular Biology. He has established valuable partnerships with leading institutions, such as Partnership for Advanced Computing in Europe (PRACE, Biodegrading Plastics – 2019215204) and Oak Ridge Leadership Computing Facility (OLCF-USA, projects CHM150, CHM151), helping secure access to over 60 million core-hours of computational resources. He served as a principal investigator (PI) for two submitted projects to the national high-performance computing (HPC) infrastructure and is currently co-PI on another (2.5 million core-hours, 2023.10904.CPCA.A2), focusing on a peripheral membrane enzyme involved in sulfide-to-sulfur conversion. João's commitment to knowledge dissemination is evident through presentations at over 10 national and international conferences. His managerial experience is substantial, involving scientific and evaluation report writing, event organization, international project evaluation, and mentoring research students at master's and Ph.D. levels (over 10 students). Notably, his mentoring extends to international students from France, Morocco, and Spain. Beyond research, João actively contributes to the peer review process for leading journals, including those published by ACS, Elsevier, and RSC. He serves as a review editor for Frontiers in Chemistry (Medicinal and Pharmaceutical Chemistry branch) and was an external reviewer for the 2019 FONDECYT Regular Competition (CONICYT, Chile), supporting high-quality international research.
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Identification

Personal identification

Full name
João Tiago Soares Coimbra

Citation names

  • Coimbra, João TS

Author identifiers

Ciência ID
AB1A-C75A-A11A
ORCID iD
0000-0001-9138-7498

Addresses

  • LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Porto, Portugal (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Biochemistry
  • Natural sciences - Biological Sciences - Biophysics
  • Exact Sciences - Chemical Sciences - Physical Chemistry

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2013/06/01 - 2017/06/01
Concluded
 PhD in Sustainable Chemistry (Doutoramento)
Universidade do Porto, Portugal

Universidade Nova de Lisboa, Portugal
"Drug transport across cell membranes" (THESIS/DISSERTATION)
 Approved
2009/10/07 - 2011/10/31
Concluded
 Master in Biochemistry (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
"Parameterization of Lipidic Components for Computational Simulation of Biomembranes through Molecular Dynamics" (THESIS/DISSERTATION)
 18/20
2006/09 - 2009/07/24
Concluded
 Bachelor in Biochemistry (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
15/20
Affiliation

Science

Category
Host institution 		Employer
2020/06/01 - Current Contracted Researcher (Research) REQUIMTE, Portugal
Universidade do Porto Faculdade de Ciências, Portugal
2019/04/01 - 2020/05/31 Postdoc (Research) Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal
(...)
2017/07/01 - 2019/03/31 Postdoc (Research) Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
(...)
2011/12/01 - 2013/05/31 Research Trainee (Research) Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
(...)
2010/09/01 - 2011/08/31 Research Trainee (Research) Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
(...)
2008/12/01 - 2009/11/30 Research Trainee (Research) Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
Universidade do Porto Unidade Multidisciplinar de Investigação Biomédica, Portugal

Others

Category
Host institution 		Employer
2013/06/01 - 2017/06/01 PhD student Fundação para a Ciência e a Tecnologia, Portugal
REQUIMTE, Portugal
(...)
Projects

Grant

Designation Funders
2013/06/01 - 2017/06/01 Drug Transport Across Cell Membranes
SFRH/BD/87434/2012
PhD Student Fellow
REQUIMTE, Portugal

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

Contract

Designation Funders
2020/06/01 - 2026/05/31 A Two-Front Approach to Tackle Antibiotic Resistance: New Drug Scaffolds for Antibiotic-modifying Enzymes and Bypassing Efflux Mechanisms
CEECIND/01374/2018/CP1545/CT0003
10.54499/CEECIND/01374/2018/CP1545/CT0003
Principal investigator
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/01 - 2025/12/31 Associated Laboratory for Green Chemistry - Clean Technologies and Processes
LA/P/0008/2020
Researcher
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Associação para a Inovação e Desenvolvimento da FCT, Portugal

Universidade de Évora, Portugal

Unidade de Investigação Vidro e Cerâmica para as Artes, Portugal

Universidade de Aveiro, Portugal

Universidade NOVA de Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2024/06/01 - 2025/05/31 Atomistic and thermodynamic characterization of the capabilities of bacterial sulfide:quinone reductase on the conversion of pollutant sulfide to elemental sulfur
2023.10904.CPCA
Co-Principal Investigator (Co-PI)
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia

Rede Nacional de Computação Avançada
Ongoing
2024/01/15 - 2024/04/14 Understanding the oligomeric assembly of Lys49 sPLA2-like phospholipases in search of their mechanism of action
2023.10650.CPCA
Principal investigator
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia

Rede Nacional de Computação Avançada
Concluded
2023/09/01 - 2024/03/31 Modeling a competent complex of a bacterial sulfide:quinone reductase interacting with its membrane counterpart
2023.09563.CPCA.A1
Co-Principal Investigator (Co-PI)
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia

Rede Nacional de Computação Avançada
Concluded
2022/06/01 - 2023/11/12 The mechanism of action of the sPLA2-like toxin of viper venom
2021.09753.CPCA
Researcher
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2023/02/02 - 2023/08/02 Exploring the interactions of a streptogramin B antibiotic to an antibiotic degrading enzyme, to devise new strategies to tackle antibiotic resistance
2022.15843.CPCA.A1
Principal investigator
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia

Rede Nacional de Computação Avançada
Concluded
2019/04/01 - 2020/05/31 UCiBio - Unidade de Ciências Biomoleculares Aplicadas
UID/Multi/04378/2019
Post-doc Fellow
REQUIMTE, Portugal

Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
Fundação para a Ciência e Tecnologia
Concluded
2017/07/01 - 2019/03/31 BioTecHealth, New Technologies for three Health Challenges of Modern Societies: Diabetes, Drug Abuse and Kidney Diseases
NORTE-01-0145-FEDER-000024
Post-doc Fellow
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal

Universidade do Porto Faculdade de Ciências, Portugal
Comissao de Coordenacao e Desenvolvimento Regional do Norte
Concluded
2012/12/01 - 2013/05/31 New Biomolecular Force Field
PTDC/QUI-QUI/103118/2008
Integration into Research Grant Fellow
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal

Universidade do Porto Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010/09/01 - 2011/08/31 Novel Key Molecular Architectures to Target Infection
PTDC/QUI/67915/2006
Master Student Fellow
Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal

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

Other

Designation Funders
2020/04/01 - 2022/10/01 Biodegrading plastic
2019215204
Post-doc
Universidade do Porto Faculdade de Ciências, Portugal
 Partnership for Advanced Computing In Europe
Concluded
2019/04 - 2020/05 Local and collective motions as a gateway to the catalytic power of enzymes
CHM150
Post-doc
Universidade do Porto Faculdade de Ciências, Portugal
 Oak Ridge National Laboratory
Concluded
2019/04 - 2020/05 Enzyme instantaneous disorder as a key player in the catalytic power of enzymes
CHM151
Post-doc
Universidade do Porto Faculdade de Ciências, Portugal
 Oak Ridge National Laboratory
Concluded
2019/09/20 - 2019/11/20 Biodegrading Plastics (Preparatory)
2010PA5065
Post-doc
Universidade do Porto Faculdade de Ciências, Portugal
 Partnership for Advanced Computing In Europe
Concluded
Outputs

Publications

Book chapter
  1. Brás, NF; Coimbra, João TS; Neves, RPP; Cerqueira, NMFSA; Sousa, SF; Fernandes, PA; Ramos, MJ. "Computational Biochemistry". Elsevier, 2015.
    https://doi.org/10.1016/B978-0-12-409547-2.10833-9
Conference abstract
  1. Gameiro, Paula; Sousa, Carla F.; Coimbra, João T.S.; Fernandes, Pedro A.; Ramos, Maria J.. "Drug Permeation Across the Bacterial Membrane: Combining Theoretical and Experimental Approaches". 2019.
    10.1016/j.bpj.2018.11.1138
  2. Sousa, Carla F; Coimbra, João TS; Ferreira, M; Fernandes, Pedro A; Gameiro, P. "Exploring the permeation of free and copper-complexed fluoroquinolones across the bacterial membrane". Paper presented in 19th IUPAB Congress / 11th EBSA Congress, Edinburgh, 2017.
    Published
Conference paper
  1. Sousa, Sérgio F; Coimbra, João T. S.; Fernandes, Pedro A.; Marino, Tiziana; Ramos, Maria J.; Russo, Nino. "Molecular Dynamics Analysis of FAAH Complexed with Anandamide". Paper presented in 18th International Workshop on Quantum Systems in Chemistry, Physics, and Biology (QSCP XVIII), Rio de Janeiro, 2013.
    Published • 10.1007/978-3-319-14397-2_7
Conference poster
  1. Magalhães, Beatriz T; Coimbra, João TS; Santos, Rita S; Azevedo, Nuno F; Fernandes, Pedro A. "Evaluating the diffusion of NAMs across the bacterial envelope". Paper presented in 5th Doctoral Congress in Engineering, 2023.
  2. Coimbra, João TS; Fernandes, Pedro A; Ramos, Maria J. "A Computational Study on the Impact of Molecular Properties on the Thermodynamics of Water Membrane Translocation". Paper presented in Open source software for enhanced-sampling simulations, 2019.
  3. Sousa C; Coimbra JTS; Ramos MJ; Fernandes PA; Gameiro P. "Combining Theoretical and Experimental Approaches to Understand the Mechanism of Drug Permeation in Bacterial Membranes: implications on the combat against bacterial resistance". Paper presented in 12th EBSA 10th ICBP-IUPAP Congress, 2019.
  4. Simões, I; Costa, I; Coimbra, João TS; Ramos, MJ; Fernandes, PA. "Improved Parameters in MM/PBSA Calculations Applied to Computational Alanine Scanning Mutagenesis". Paper presented in IV Encontro de Jovens Investigadores de Biologia Computacional Estrutural, 2016.
  5. Silva, AMN; de Castro MMFPM; Oliveira ADA; Brás, NF; Coimbra, João TS; Fernandes, PA; Ramos, MJ; Rangel, M. "Implications for Iron-binding of Human Holo-transferrin Glycation". Paper presented in 11th Inorganic Chemistry Conference, 2016.
  6. Coimbra, João TS; Fernandes, PA; Ramos, MJ. "Revisiting Partition in Hydrated Bilayer Systems". Paper presented in DYNAPEUTICS international summer school, 2016.
  7. Teixeira, N; Fernandes, I; Coimbra, João TS; Brás, NF; Mateus, N; de Freitas, V; Oliveira, J. "The Influence of the Self-Association Effect on the Anthocyanin Copigmentation Mechanism". Paper presented in XXVIIIth Internatioal Conference on Polyphenols (ICP 2016), 2016.
  8. Coimbra, João TS; Brás, NF; Fernandes, PA; Rangel, M; Ramos, MJ. "Relevant Interactions Of Potential Drugs and Membrane Models Revealed by Molecular Dynamics Simulations". Paper presented in CECAM Workshop: Binding free energy and kinetics: computation meets experiments, 2014.
  9. Noronha-Matos, JB; Sa-E-Sousa, A; Coimbra J; Gomes S; Marinhas J; Rocha R; Freitas R; et al. "The P2X7 Receptor May Be a Novel Therapeutic Target to Promote Osteogenic Differentiation and Mineralization of Postmenopausal Bone Marrow Stromal Cells". Paper presented in 6th European Congress of Pharmacology EPHAR, 2012.
  10. Noronha-Matos, JB; Sá-e-Sousa, A; Coimbra, João TS; Gomes, S; Rocha, R; Marinhas, J; Freitas, R; et al. "P2X7 Receptor-induced Osteogenic Differentiation of Postmenopausal Bone Marrow Stromal Cells Depends on Rho-kinase Activation and Cytoskeleton Rearrangements". Paper presented in Purines Meeting, 2012.
  11. Coimbra, João TS; Sousa, SF; Fernandes, PA; Rangel, M; Ramos, MJ. "Parameterization of Lipid Components for Molecular Dynamics Simulations of Biomembranes". Paper presented in 5th symposium on Theoretical Biophysics, 2011.
  12. Coimbra, João TS; Sousa, SF; Fernandes, PA; Ramos, MJ; Rangel, M. "New Architectures to Fight Infectious Diseases under a Computational Themed Perspective". Paper presented in 2nd Iberic Meeting on Medicinal Chemistry: G Protein-Coupled Receptors and Enzymes in Drug Discovery, 2011.
  13. Coimbra, João TS; Sousa, SF; Fernandes, PA; Rangel, M; Ramos, MJ. "Computational Studies of the Interaction Between Phospholipid Bilayers and Potential New Drugs". Paper presented in 4th Meeting of Young Researchers of University of Porto (IJUP 2011), 2011.
Journal article
  1. Beatriz T. Magalhães; João T. S. Coimbra; Raquel M. Silva; Mariana Ferreira; Rita S. Santos; Paula Gameiro; Nuno F. Azevedo; Pedro A. Fernandes. "Crosstalk of Nucleic Acid Mimics with Lipid Membranes: A Multifaceted Computational and Experimental Study". Biochemistry (2024): https://doi.org/10.1021/acs.biochem.4c00349.
    10.1021/acs.biochem.4c00349
  2. João T. S. Coimbra; Antoine Gissler; Emiel Nitor; Kiana Rostamipour; Ana V. Cunha; Maria J. Ramos; Pedro A. Fernandes. "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2-like Peptides". JACS Au (2024): https://doi.org/10.1021/jacsau.4c00646.
    10.1021/jacsau.4c00646
  3. João T. S. Coimbra; Pedro A. Fernandes; Maria J. Ramos. "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations". Journal of Chemical Information and Modeling (2023): https://doi.org/10.1021/acs.jcim.3c00962.
    10.1021/acs.jcim.3c00962
  4. How Chee Ong; João T. S. Coimbra; Maria J. Ramos; Bengang Xing; Pedro A. Fernandes; Felipe García. "Beyond the TPP+ “gold standard”: a new generation mitochondrial delivery vector based on extended PN frameworks". Chemical Science (2023): https://doi.org/10.1039/D2SC06508H.
    10.1039/D2SC06508H
  5. João T. S. Coimbra; Rui P. P. Neves; Ana V. Cunha; Maria J. Ramos; Pedro A. Fernandes. "Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease". Chemistry – A European Journal (2022): https://doi.org/10.1002/chem.202201066.
    10.1002/chem.202201066
  6. João T. S. Coimbra; Rui P. P. Neves; Ana V. Cunha; Maria J. Ramos; Pedro A. Fernandes. "Cover Feature: Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease (Chem. Eur. J. 42/2022)". Chemistry – A European Journal (2022): https://doi.org/10.1002/chem.202202001.
    10.1002/chem.202202001
  7. Luís M. C. Teixeira; João T. S. Coimbra; Maria João Ramos; Pedro Alexandrino Fernandes. "Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic". Journal of Chemical Information and Modeling (2022): https://doi.org/10.1021/acs.jcim.1c01561.
    10.1021/acs.jcim.1c01561
  8. Sousa, Carla F.; Coimbra, João T.S.; Richter, Robert; Morais-Cabral, João H.; Ramos, Maria J.; Lehr, Claus-Michael; Fernandes, Pedro A.; Gameiro, Paula. "Exploring the permeation of fluoroquinolone metalloantibiotics across outer membrane porins by combining molecular dynamics simulations and a porin-mimetic in vitro model". Biochimica et Biophysica Acta (BBA) - Biomembranes 1864 3 (2022): 183838. http://dx.doi.org/10.1016/j.bbamem.2021.183838.
    Published • 10.1016/j.bbamem.2021.183838
  9. Sousa, Carla F.; Coimbra, João TS; Ferreira, Mariana; Pereira-Leite, Catarina; Reis, Salette; Ramos, Maria J.; Fernandes, Pedro A.; Gameiro, Paula. Corresponding author: Fernandes, Pedro A.. "Passive Diffusion of Ciprofloxacin and its Metalloantibiotic: A Computational and Experimental study". Journal of Molecular Biology 433 9 (2021): 166911. http://dx.doi.org/10.1016/j.jmb.2021.166911.
    Published • 10.1016/j.jmb.2021.166911
  10. João T. S. Coimbra; Ralph Feghali; Rui P. Ribeiro; Maria J. Ramos; Pedro A. Fernandes. "The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer". RSC Advances (2021): https://doi.org/10.1039/D0RA09995C.
    10.1039/D0RA09995C
  11. How Chee Ong; João T. S. Coimbra; Germain Kwek; Maria J. Ramos; Bengang Xing; Pedro A. Fernandes; Felipe García. "Alkyl vs. aryl modifications: a comparative study on modular modifications of triphenylphosphonium mitochondrial vectors". RSC Chemical Biology (2021): https://doi.org/10.1039/D1CB00099C.
    10.1039/D1CB00099C
  12. How Chee Ong; Zhang Hu; João T. S. Coimbra; Maria J. Ramos; Oi Lian Kon; Bengang Xing; Edwin K. L. Yeow; Pedro A. Fernandes; Felipe García. "Enabling Mitochondrial Uptake of Lipophilic Dications Using Methylated Triphenylphosphonium Moieties". Inorganic Chemistry (2019): https://doi.org/10.1021/acs.inorgchem.8b03380.
    10.1021/acs.inorgchem.8b03380
  13. Coimbra, J.T.S.; Brás, N.F.; Fernandes, P.A.; Rangel, M.; Ramos, M.J.. "A computational study on the redox properties and binding affinities of iron complexes of hydroxypyridinones". Journal of molecular modeling 25 6 (2019): 172-172. http://www.scopus.com/inward/record.url?eid=2-s2.0-85066929697&partnerID=MN8TOARS.
    10.1007/s00894-019-4037-0
  14. Friedman, Ran; Khalid, Syma; Aponte-Santamaría, Camilo; Arutyunova, Elena; Becker, Marlon; Boyd, Kevin J.; Christensen, Mikkel; et al. "Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology". The Journal of Membrane Biology 251 5-6 (2018): 609-631. http://dx.doi.org/10.1007/s00232-018-0050-y.
    Published • 10.1007/s00232-018-0050-y
  15. Silva, A.M.N.; Coimbra, J.T.S.; Castro, M.M.; Oliveira, Â.; Brás, N.F.; Fernandes, P.A.; Ramos, M.J.; Rangel, M.. "Determining the glycation site specificity of human holo-transferrin". Journal of Inorganic Biochemistry 186 (2018): 95-102. http://www.scopus.com/inward/record.url?eid=2-s2.0-85047838148&partnerID=MN8TOARS.
    10.1016/j.jinorgbio.2018.05.016
  16. João T. S. Coimbra; Natércia F. Brás; Pedro A. Fernandes; Maria Rangel; Maria J. Ramos. "Membrane partition of bis-(3-hydroxy-4-pyridinonato) zinc(ii) complexes revealed by molecular dynamics simulations". RSC Advances (2018): https://doi.org/10.1039/C8RA03602K.
    10.1039/C8RA03602K
  17. João T. S. Coimbra; Inês C. M. Simões; Rui P. P. Neves; Inês P. D. Costa; Maria J. Ramos; Pedro A. Fernandes. "Properties that rank protein:protein docking poses with high accuracy". Physical Chemistry Chemical Physics (2018): https://doi.org/10.1039/C8CP03888K.
    10.1039/C8CP03888K
  18. João T. S. Coimbra; Pedro A. Fernandes; Maria J. Ramos. "Revisiting Partition in Hydrated Bilayer Systems". Journal of Chemical Theory and Computation 13 5 (2017): 2290-2299. https://doi.org/10.1021/acs.jctc.6b01258.
    10.1021/acs.jctc.6b01258
  19. Ribeiro, R.P.; Coimbra, J.T.S.; Ramos, M.J.; Fernandes, P.A.. "Diffusion of the small, very polar, drug piracetam through a lipid bilayer: an MD simulation study". Theoretical Chemistry Accounts 136 4 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85015706251&partnerID=MN8TOARS.
    10.1007/s00214-017-2073-3
  20. Sousa, C.F.; Coimbra, J.T.S.; Gomes, I.; Franco, R.; Fernandes, P.A.; Gameiro, P.. "The binding of free and copper-complexed fluoroquinolones to OmpF porins: an experimental and molecular docking study". RSC Advances 7 17 (2017): 10009-10019. http://www.scopus.com/inward/record.url?eid=2-s2.0-85012008929&partnerID=MN8TOARS.
    10.1039/C6RA26466B
  21. Simões, I.C.M.; Costa, I.P.D.; Coimbra, J.T.S.; Ramos, M.J.; Fernandes, P.A.. "New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces". Journal of Chemical Information and Modeling 57 1 (2017): 60-72. http://www.scopus.com/inward/record.url?eid=2-s2.0-85014019791&partnerID=MN8TOARS.
    10.1021/acs.jcim.6b00378
  22. Moniz, T.; Coimbra, J.T.S.; Brás, N.F.; Cunha-Silva, L.; Ramos, M.J.; Fernandes, P.A.; De Castro, B.; Rangel, M.. "Synthesis and structural characterization, by spectroscopic and computational methods, of two fluorescent 3-hydroxy-4-pyridinone chelators bearing sulphorhodamine B and naphthalene". RSC Advances 6 5 (2016): 4200-4211. http://www.scopus.com/inward/record.url?eid=2-s2.0-84954288404&partnerID=MN8TOARS.
    10.1039/c5ra23217a
  23. Moreira, I.S.; Martins, J.M.; Coimbra, J.T.S.; Ramos, M.J.; Fernandes, P.A.. "A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy". Physical Chemistry Chemical Physics 17 4 (2015): 2378-2387. http://www.scopus.com/inward/record.url?eid=2-s2.0-84919807951&partnerID=MN8TOARS.
    10.1039/c4cp04688a
  24. Coimbra, J.T.S.; Moniz, T.; Brás, N.F.; Ivanova, G.; Fernandes, P.A.; Ramos, M.J.; Rangel, M.. "Relevant interactions of antimicrobial iron chelators and membrane models revealed by nuclear magnetic resonance and molecular dynamics simulations". Journal of Physical Chemistry B 118 50 (2014): 14590-14601. http://www.scopus.com/inward/record.url?eid=2-s2.0-84919389836&partnerID=MN8TOARS.
    10.1021/jp509491p
  25. Coimbra, J.T.S.; Neves, R.P.P.; Passos, Ó.; Jarukanont, D.; Fernandes, P.A.; Patel, S.; Garcia, M.E.; Ramos, M.J.. "Influence of the environment on protein bond energies". Chemical Physics Letters 615 (2014): 75-82. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908192323&partnerID=MN8TOARS.
    10.1016/j.cplett.2014.09.066
  26. Silva, A.M.N.; Sousa, P.R.H.; Coimbra, J.T.S.; Brás, N.F.; Vitorino, R.; Fernandes, P.A.; Ramos, M.J.; Rangel, M.; Domingues, P.. "The glycation site specificity of human serum transferrin is a determinant for transferrin's functional impairment under elevated glycaemic conditions". Biochemical Journal 461 1 (2014): 33-42. http://www.scopus.com/inward/record.url?eid=2-s2.0-84902345071&partnerID=MN8TOARS.
    10.1042/BJ20140133
  27. Coimbra, J.T.S.; Sousa, S.F.; Fernandes, P.A.; Rangel, M.; Ramos, M.J.. "Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble". Journal of Biomolecular Structure and Dynamics 32 1 (2014): 88-103. http://www.scopus.com/inward/record.url?eid=2-s2.0-84889680410&partnerID=MN8TOARS.
    10.1080/07391102.2012.750250
  28. Noronha-Matos, J.B.; Coimbra, J.; Sá-e-Sousa, A.; Rocha, R.; Marinhas, J.; Freitas, R.; Guerra-Gomes, S.; et al. "P2X7-induced zeiosis promotes osteogenic differentiation and mineralization of postmenopausal bone marrow-derived mesenchymal stem cells". FASEB Journal 28 12 (2014): 5208-5222. http://www.scopus.com/inward/record.url?eid=2-s2.0-84919754255&partnerID=MN8TOARS.
    10.1096/fj.14-257923
  29. Jarukanont, D.; Coimbra, J.T.S.; Bauerhenne, B.; Fernandes, P.A.; Patel, S.; Ramos, M.J.; Garcia, M.E.. "Biomolecular structure manipulation using tailored electromagnetic radiation: A proof of concept on a simplified model of the active site of bacterial DNA topoisomerase". Physical Chemistry Chemical Physics 16 39 (2014): 21768-21777. http://www.scopus.com/inward/record.url?eid=2-s2.0-84907833756&partnerID=MN8TOARS.
    10.1039/c4cp02289k
  30. 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
  31. Sousa, S.F.; Coimbra, J.T.S.; Paramos, D.; Pinto, R.; Guimarães, R.S.; Teixeira, V.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif". Journal of Molecular Modeling 19 2 (2013): 673-688. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877128216&partnerID=MN8TOARS.
    10.1007/s00894-012-1590-1
  32. 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
Magazine article
  1. Coimbra, João TS. "Proteínas Virais no Protein Data Bank", Revista de Ciência Elementar, 2020, https://rce.casadasciencias.org/rceapp/art/2020/022/.
Thesis / Dissertation
  1. João Tiago Soares Coimbra. "Drug transport across cell membranes". PhD, 2017. http://hdl.handle.net/10216/104421.
  2. Coimbra, João TS. "Parameterization of Lipidic Components for Computational Simulation of Biomembranes through Molecular Dynamics". Master, Universidade do Porto Faculdade de Ciências, 2011.

Other

Dataset
  1. Coimbra, João TS. Dataset from "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2-like Peptides". Zenodo. 2024.
  2. Coimbra, João TS; Fernandes, Pedro Alexandrino; Ramos, Maria João. Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations". Zenodo. 2023.
    https://doi.org/10.5281/zenodo.8255787
Other output
  1. Alkyl vs Aryl Modifications: A Comparative Study on Modular Modifications of Triphenylphosphonium Mitochondrial Vectors. 2021. How Chee Ong; João T.S. Coimbra; Maria Joa~o Ramos; Bengang Xing; Pedro Alexandrino Fernandes; Felipe Garcia. https://doi.org/10.26434/chemrxiv.14445327.
    10.26434/chemrxiv.14445327
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/08/30 Direct Involvement of the C-terminal Region of Bothrops asper Lys49 Phospholipase A2-like protein in Ca2+ translocation: a molecular dynamics study Peptides in biology and materials: bridging simulation and experimental data
CECAM-IT-SIMUL (Florence, Italy)
2020/02/26 Computational Biochemistry: From Protein Dynamics to Membrane Translocation DQB Seminars 2020
Department of Chemistry and Biochemistry, Faculty of Sciences of University of Porto (Porto, Portugal)
2019/08/23 Computational Biochemistry: Membrane Studies Course of Computational Biochemistry for the Masters in Biochemistry
FCUP (Porto, Portugal)
2018/10/08 Membrane Partition of Transition Metal Complexes Explored by Molecular Dynamics Simulations 44th International Congress of Theoretical Chemists of Latin Expression (QUITEL 2018)
Centro de Extensión UC Pontificia Universidad Católica de Chile (Santiago, Chile)
2018/04/23 Computational Approaches to Predict and Refine the Structure of Proteins Structural Biology Course for the GABBA PhD Program
I3S (Porto, Portugal)
2018/04/19 Lecture on Molecular Docking and Molecular Dynamics Simulations Course of Medicinal Chemistry
(Porto, Portugal)
2015/04/30 Lecture on Molecular Dynamics Simulations: Biological Membranes Course of Computational Biological Chemistry
(Porto, Portugal)
2014/05/29 Lecture on Molecular Dynamics Simulations: Protein Denaturation and Membrane Translocation Course of Computational Biological Chemistry
(Porto, Portugal)
2012/06 Drug Interaction with Hydrated Glycerophospholipid Bilayers 2nd EBSA Biophysics Course on: Membrane Biophysics and Lipid-Protein Interaction
(Bordeaux-Lacanau, France)
2012/05 Conception of Glycerophospholipid Hydrated Bilayer Models through Computational Modeling 3rd Portuguese Young Chemists Meeting (3PYCheM)
Sociedade Portuguesa de Química (Porto, Portugal)
2012/02 New Biomolecular Force Field: Lipid Components 5th Meeting of Young Researchers of University of Porto (IJUP 2012)
University of Porto (Porto, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023/09 - 2024/11/25 The molecular mechanism of membrane disruption by snake venom PLA2-like proteins
Co-supervisor
 Master in Applications in Biotechnology and Synthetic Biology (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2020/02/11 - 2020/07/22 Computational prevision of safranal affinity to trypsin and a-chymotrypsin and posible structural changes
Co-supervisor
 Chemistry (Degree)
Universidade do Porto Faculdade de Ciências, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2019/11/13 - 2019/12/31 9th Edition of the "Moléculas Magníficas" Art exhibition (2019/11/13 - 2019/12/31)
Exhibition (Member of the Organising Committee)
 Universidade do Porto, Portugal
2016/09/05 - 2016/10/01 11th Intensive Course of the European Master in Theoretical Chemistry and Computational Modelling (2016/09/05 - 2016/10/01)
Workshop (Other)
 Universidade do Porto Faculdade de Ciências, Portugal
2016/02/17 - 2016/02/19 Collaborator in a meeting of young researchers of University of Porto (IJUP) (2016/02/17 - 2016/02/19)
Meeting (Other)
 Universidade do Porto, Portugal
2015/05/13 - 2015/05/15 Collaborator in a meeting of young researchers of University of Porto (IJUP) (2015/05/13 - 2015/05/15)
Meeting (Other)
 Universidade do Porto, Portugal
2012/05/04 - 2012/05/08 Member of the local organizing committee of the CODECS/COST action meeting (2012/05/04 - 2012/05/08)
Meeting (Member of the Organising Committee)
 Universidade do Porto Faculdade de Ciências, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2023/11/07 - 2024/02/11 Contribution to an art exhibition at the University of Porto's rectory entitled: 'Snakes - A Relationship of Love and Fear with Humanity', targeting a general audience, and showcasing the 3D structure of snake toxins.
Exhibition
 Snakes - A Relationship of Love and Fear with Humanity
Universidade do Porto Faculdade de Ciências, Portugal

REQUIMTE LAQV Porto, Portugal
2022/11/14 - 2022/11/18 Participation in the European University Alliance for Global Health (EUGLOH) course 'Tumor immunology and immunotherapy of cancer'.
Workshop
 Tumor Immunology and Immunotherapy of Cancer
Université Paris-Saclay, France
2021/09/30 - 2021/10/01 Participation in the 2nd TIMB3 Symposium "The Role of Dynamics in Biocatalysis and the Methods to Study it".
Symposium
 TIMB3 Mini Symposium: The Role of Dynamics in Biocatalysis and the Methods to Study it
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/04/23 - 2021/04/24 Participation in the Hünfeld Online Workshop 'Computer Simulation and Theory of Macromolecules'
Workshop
 Online Workshop on Computer Simulation and Theory of Macromolecules
Max Planck Institute for Multidisciplinary Sciences, Germany
2019/07/22 - 2019/07/27 CECAM workshop and school on open source software for enhanced-sampling simulations.
Workshop
 Open source software for enhanced-sampling simulations
Centre Européen de Calcul Atomique et Moléculaire (CECAM), Switzerland
2019/06/10 - 2019/06/13 PRACE/BioExcel Seasonal School 2019
Workshop
 HPC for Life Sciences
Partnership for Advanced Computing In Europe, Belgium

BioExcel Center of Excellence for Computational Biomolecular Research, Sweden
2017/07/12 - 2017/07/12 Workshop on innovation and intellectual property
Workshop
 Workshop on innovation and intellectual property
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal
2016/09/25 - 2016/09/30 DYNAPEUTICS international summer school
Workshop
 DYNAPEUTICS international summer school
2016/03/17 - 2016/03/20 Science, Teaching and Innovation Fair of University of Porto
Exhibition
 14th University Fair of University of Porto
Universidade do Porto Faculdade de Ciências, Portugal
2015/07/06 - 2015/07/10 Teaching Chemistry to High-school Students
Other
 Chemistry and Biochemistry School 2015
2014/07/14 - 2014/07/18 Teaching Chemistry to High-school Students
Other
 Chemistry an Biochemistry School 2014
Universidade do Porto Faculdade de Ciências, Portugal
2014/06/10 - 2014/06/12 CECAM workshop: Binding free energy and kinetics - computation meets experiments
Workshop
 CECAM workshop: Binding free energy and kinetics - computation meets experiments
Istituto Italiano di Tecnologia, Italy
2014/05/21 - 2014/05/23 3rd Annual CCP-BioSim Conference: Frontiers of Biomolecular Simulation
Conference
 3rd Annual CCP-BioSim Conference: Frontiers of Biomolecular Simulation
The University of Edinburgh School of Chemistry, United Kingdom
2013 - 2013 Hands on course: NMR in protein interactions studies
Workshop
 Hands on course: NMR in protein interactions studies
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2012/06/24 - 2012/06/29 2nd EBSA biphysics course on: membrane biophysics and lipid protein interaction
Workshop
 2nd EBSA biphysics course on: membrane biophysics and lipid protein interaction
2012/05/09 - 2012/05/11 3rd Portuguese Young Chemists Meeting (3PYCheM)
Meeting
 3rd Portuguese Young Chemists Meeting (3PYCheM)
Universidade do Porto Faculdade de Ciências, Portugal
2012/02/22 - 2012/02/24 5th Meeting of Young Researchers of University of Porto (IJUP 2012)
Meeting
 5th Meeting of Young Researchers of University of Porto (IJUP 2012)
Universidade do Porto, Portugal
2011/06/12 - 2011/06/15 2nd Iberic Meeting on Medicinal Chemistry: G Protein-Coupled Receptors and Enzymes in Drug Discovery
Meeting
 2nd Iberic Meeting on Medicinal Chemistry: G Protein-Coupled Receptors and Enzymes in Drug Discovery
Universidade do Porto Faculdade de Ciências, Portugal
2011/06/08 - 2011/06/11 5th symposium on Theoretical Biophysics
Symposium
 5th symposium on Theoretical Biophysics
2011/02/17 - 2011/02/19 4th Meeting of Young Researchers of University of Porto (IJUP 2011)
Meeting
 4th Meeting of Young Researchers of University of Porto (IJUP 2011)
Universidade do Porto, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2024/12/05 Designing Optimal 3D Enzyme Computational Models for Efficient Plastic Degradation
(Thesis) Main arguer
 Mariana Gomes Fernandes (Master)
Universidade do Porto, Portugal
2021/11/11 Enzymatic Technologies for Cleaning Petroleum with Low CO2 Emissions
(Thesis) Main arguer
 Bruno Miguel Viveiros Araújo (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2020/11/10 Understanding Phosphoenolpyruvate carboxylase catalysis as a step to the engineering of a CO2 capture device
(Thesis) Main arguer
 Rita Maria Bolota Velho Pires da Fonseca (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2024 - 2024 International Journal of Molecular Sciences MDPI
2023 - 2024 International Journal of Peptide Research and Therapeutics Springer
2023 - 2024 Journal of Biomolecular Structure and Dynamics Taylor & Francis Online
2023 - 2023 Computational and Structural Biotechnology Journal Elsevier
2019 - 2022 Journal of Chemical Information and Modeling American Chemical Society
2021 - 2021 RSC Advances Royal Society of Chemistry
2021 - 2021 Chemical Physics Letters Elsevier
2020 - 2020 Journal of Molecular Graphics and Modelling Elsevier

Consulting

Activity description Institution / Organization
2013/09 - 2014/12 Young research consultant for a food industry company (PepsiCo). PepsiCo Global Research and Development, United States

Mentoring / Tutoring

Topic Student name
2024 - Current Computational Studies on Topoisomerase I Inhibitors Angela Trejo
2022/03/01 - 2024/12/01 Computational Modelling of Diffusion and Hybridization of Nucleic Acid Mimics Beatriz Magalhães
2020/09 - 2023/06 Molecular Dynamics Simulations of protein:ligand complexes and reaction mechanisms of proteases Luís Teixeira
2022/04/01 - 2022/09/01 The mechanism of action of the sPLA2-like toxin of viper venom Antoine Gissler
2021/09/01 - 2022/01/31 Molecular Dynamics simulations of Proteins involved in SARS-CoV-2 infection mechanisms Mehdi Oubahmane
2015/02 - 2020/07 Membrane Biophysics and Transport of Antibiotics Carla F. Sousa
2020/02 - 2020/05 Examining the Effects of Increasing Alkyl Chain Length as Well as Aryl Group Size in the Translocation of Triphenylphosphonium Cations Sonata Kvedaraviciute
2019/04/01 - 2019/08/01 The importance of intramolecular hydrogen bonding on the passive diffusion through a lipid bilayer: an MD simulation study Ralph Feghali
2018/02 - 2018/05 Molecular Dynamics Modelling of the Fluorescence Behaviour of Tagged SecA Protein Pei-Yi Chen
2016/10 - 2017/01 QM/MM studies on the Structure and Reactivity of Cytochrome P450 enzymes Elisa Bernes
2015/07 - 2016/12 Protein:Protein Interactions and the Prediction of Native Poses of Protein:Protein Complexes Inês Simões
2015/07 - 2016/01 Protein:Protein Interactions and the Prediction of Native Poses of Protein:Protein Complexes Inês Costa
2014/02 - 2015/12 Membrane Transport of Small Drug-like Compounds Rui Pedro Ribeiro

Other jury / evaluation

Activity description Institution / Organization
2023/12 - Current Editorial office roles as a review editor for the Frontiers in Chemistry journal
2024/07/08 - 2024/07/08 Participated in the evaluation of a internship report (first degree in Biochemistry), assessing research quality, data interpretation, and the effectiveness of scientific communication. Universidade do Porto Faculdade de Ciências, Portugal
2018/12/17 - 2018/12/20 I have participated as an external reviewer for proposals submitted to the 2019 FONDECYT Regular Competition (CONICYT, Chile). Comisión Nacional de Investigación Científica y Tecnológica, Chile