João Tiago Soares Coimbra (AB1A-C75A-A11A)

Curriculum Vitae

João Tiago Soares Coimbra

João T. S. COIMBRA is a recognized researcher at the Portuguese Research Centre for Sustainable Chemistry (LAQV, REQUIMTE). His current research focuses on applying multi-resolution computational methods to explore the molecular mechanisms responsible for antimicrobial resistance, specifically studying antibiotic modification and degradation by enzymes. He graduated in Biochemistry and earned his PhD in Sustainable Chemistry in 2017 from the Universities of Nova Lisbon and Porto, gaining expertise in Computational Biochemistry. During his PhD, he conducted drug design studies, examining how drug-like molecules move through models of biological membranes. Additionally, he developed computational methods to explore protein-protein interactions. In this period, he also served as a young research consultant for PepsiCo, Inc. ----- Following his PhD, he joined the Research Unit on Applied Molecular Biosciences (UCIBIO). As a postdoctoral fellow at UCIBIO, his focus was on developing new drugs to combat type-II diabetes (project: NORTE-01-0145-FEDER-000024). In 2020, he was granted a Recognized Researcher (R2) position through the highly competitive Individual Call of the Portuguese National Science Foundation (CEEC IND 2018, FCT), a position he currently holds (https://doi.org/10.54499/CEECIND/01374/2018/CP1545/CT0003). ----- João is a multifaceted researcher actively engaging in collaborations across various fields of expertise, including inorganic chemistry, chemical synthesis, and membrane biophysics. These collaborations have been convened with several established researchers across the globe, spanning Europe (Germany, Spain, Portugal), America (USA), and Asia (Singapore). His scientific skills are highly enriched in computational methods applied to biomolecules, encompassing molecular dynamics simulations, free energy calculations, enhanced sampling methods, hybrid quantum-mechanics/molecular-mechanics approaches, and molecular docking. ----- He authored 30 indexed publications (h-index: 12, 524 total citations - scopus), including highly prestigious journals, such as Chemical Science and Journal of Molecular Biology. He actively contributes to multiple research projects at both national and international levels, collaborating with institutions/programs such as Partnership for Advanced Computing in Europe (PRACE), Oak Ridge Leadership Computing Facility (OLCF-USA), and The European High-Performance Computing (EuroHPC). He served as a principal investigator (PI) for two submitted projects to the national high-performance computing (HPC) infrastructure and is co-PI on another one. He is also the co-PI for a submitted HPC project (2.5M core-hours) currently under evaluation. ----- João's commitment to knowledge dissemination is evident through presentations at over 15 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 PhD levels (over 10 students). Notably, his mentoring extends to international students from France, Marocco, and Spain. He currently co-supervises a master's student and mentors a 4th-year PhD student from the Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE). In addition to his research contributions, João actively participates in the peer review process for various journals, including publishers such as ACS, Elsevier, and RSC. Towards the end of 2023, he assumed editorial office roles as a review editor for the Frontiers in Chemistry journal, specifically in the Medicinal and Pharmaceutical Chemistry branch. Furthermore, he was an external reviewer for proposal submitted to the 2019 FONDECYT Regular Competition (CONICYT, Chile).

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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

https://laqv.requimte.pt/people/493-joao_coimbra (Professional)

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
2023/12/19 - Current	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 Under evaluation
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
2024/01/15 - 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 Ongoing
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 Ongoing
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	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	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 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	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	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. 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. 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. 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. 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. Coimbra, João TS; Fernandes, PA; Ramos, MJ. "Revisiting Partition in Hydrated Bilayer Systems". Paper presented in DYNAPEUTICS international summer school, 2016. 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. 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. 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. 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. 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. 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. 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	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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	Coimbra, João TS. "Proteínas Virais no Protein Data Bank", Revista de Ciência Elementar, 2020, https://rce.casadasciencias.org/rceapp/art/2020/022/.
Thesis / Dissertation	João Tiago Soares Coimbra. "Drug transport across cell membranes". PhD, 2017. http://hdl.handle.net/10216/104421. 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	Coimbra, João TS. Dataset from "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2-like Peptides". Zenodo. 2024. 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	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 - Current	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
2017 - 2019	Cycle of conferences of the Theoretical and Computational Biochemistry (TCB) group (2017) Seminar (Co-organisor)	Universidade do Porto Faculdade de Ciências, 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
2018/09/28 - 2018/09/29	UCIBIO Annual Meeting Meeting	UCIBIO Annual Meeting REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal
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
2011/01/13 - 2011/01/14	REQUIMTE biennial meeting Meeting	REQUIMTE biennial meeting REQUIMTE, 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
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