???global.info.a_carregar???
I completed my BSc and MSc at the University of Porto (UP) in 2011 and began my research career in 2012 with a PhD grant by Fundação para a Ciência e Tecnologia. I got my PhD degree from UP in 2016, supervised by Prof Maria João Ramos. During my PhD, I performed force-field development, assessed density functional theory to study biochemical reactions, and characterized enzyme reaction mechanisms for drug and biomarker development. I also took part in national (Prof António Varandas, U Coimbra) and international (Prof Martin Garcia, U Kassel) collaborations. From 2017-2022, I was a postdoc fellow in the High Performance Computing in Molecular Modelling Group (within LAQV), and I have been involved in 7 funded projects either computational or multidisciplinary. I devised virtual-screening campaigns and in silico hit-to-lead development of new patentable drugs for type-II diabetes (NORTE-01-0145-FEDER-000024) in a multidisciplinary team of experimental groups: Natural Products, Chemistry and Bioactivity (Prof Paula Andrade, LAQV) and Toxicology (Prof Lourdes Bastos, UCIBIO); with the Macromolecular Crystallography group (Dr Angelina Palma, UCIBIO), I co-led a multidisciplinaryproject to assess natural compounds as novel antidiabetic drugs; and I was a team member on a multidisciplinary project to develop new antidiabetic flavonoid scaffolds (PTDC/MED-QUI/29241/2017), from the Natural Products, Chemistry and Bioactivity group (Prof Eduarda Fernandes, LAQV). More recently, I have studied enzyme reaction mechanisms of sulfur oxygenation and devised computational protocols for the in silico design of enzyme mutants for the biodesulfurization of sour crude oil (PTDC/QUI-QFI/28714/2017), together with Dr Sandra Ribeiro (I3S, Porto). I also integrated a 3-year HPC PRACE project (2019215204) focusing on PET plastic biorecycling, and two project from the Oak Ridge National Laboratory (OLCF) on the study of active site dynamics in the catalysis by human pancreatic amylase and the HIV-1 protease with QM/MM MD simulations. Currently, I am a FCT Junior researcher at the High Performance Computing in Molecular Modelling Group (Ref. 2021.00391.CEECIND/CP1662/CT0003). I am studying enzymes reaction mechanisms and developing computational protocols focused on the engineering of bacterial enzymes able to convert sulfur pollutants into non-pollutant sulfur forms. I am also the PI of one computing project in high-.performing computing facilities (Oblivion supercomputer through a project from the National Platform for Advance Computing (RNCA), 2023.09563.CPCA.A1) and the co-PI of two other (VEGA supercomputer through an EuroHPC project, EHPC-REG-2022R03-205, and the Oblivion supercomputer through a project from the National Platform for Advance Computing (RNCA), 2022.15843.CPCA.A1). In the last 5 years, I published 18 research papers in indexed peer-reviewed journals (ca. 179 citations and h-index of 8), several of them in journals with impact factors above 9 (ACS Catalysis, PNAS, Green Chemistry). I also peer-review for top journals (ACS Catalysis, Chemistry Eur J, J Phys Chem). I presented several scientific communications in international/national events, mentored/supervised over a dozen national/international students ranging MSc to PhD degress, and participated in MSc academic juries. I also participated in workshops on intellectual property protection and promoted activities within my workplace (group seminars, international conferences), took part in activities for scientific dissemination and cultural outreach within the University of Porto (University fair, scientific exhibitions) and published in open national journals for an educational audience.
Read full resume ↓
Identification

Personal identification

Full name
Rui Pedro Pimenta das Neves

Citation names

  • Neves, Rui P. P.

Author identifiers

Ciência ID
0F17-0547-ADD3
ORCID iD
0000-0003-2032-9308
Researcher Id
L-4544-2014
Scopus Author Id
36647716400

Email addresses

  • rui.neves@fc.up.pt (Professional)

Websites

Knowledge fields

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

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Proficiency (C2) Advanced (C1) Advanced (C1)
French Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Spanish; Castilian Beginner (A1) Intermediate (B1) Beginner (A1)
Portuguese (Mother tongue)
Education
Degree Classification
2012/01/01 - 2016/04/18
Concluded
 Chemistry (Doutoramento)
Major in Theoretical Chemistry and Computational Biochemistry
Universidade do Porto Faculdade de Ciências, Portugal
"Metals' Data for Biomolecular Force Fields" (THESIS/DISSERTATION)
 Approved with distinction and by unanimity
2009 - 2011
Concluded
 Physics and Chemistry Teacher Education for Middle and Secondary Schools (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
"Internship Report 2010/2011" (THESIS/DISSERTATION)
 17/20 (class B in the ECTS grading scale
2006 - 2009
Concluded
 Chemisty (Licenciatura)
Major in Chemisty (with minor in Physics)
Universidade do Porto Faculdade de Ciências, Portugal
"Partial Molar Volume: Microscopic Insight from Macroscopic Results" (THESIS/DISSERTATION)
 17/20 (class A in the ECTS grading scale
Affiliation

Science

Category
Host institution 		Employer
2022/04/01 - Current Contracted Researcher (Research) Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
REQUIMTE LAQV Porto, Portugal
(...)
2021/10/01 - 2022/03/31 Contracted Researcher (Research) REQUIMTE, Portugal
REQUIMTE LAQV Porto, Portugal
(...)
2019/04/01 - 2021/09/30 Contracted Researcher (Research) REQUIMTE, Portugal
Universidade do Porto Faculdade de Ciências, Portugal
(...)
2017/01/01 - 2019/03/31 Contracted Researcher (Research) Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
Universidade do Porto Faculdade de Ciências, Portugal
(...)
2016/05/15 - 2016/12/31 Postdoc (Research) Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal

Others

Category
Host institution 		Employer
2012/01/01 - 2015/12/31 PhD position in Theoretical Chemistry and Computational Biochemistry group of Professor Maria João Ramos Fundação para a Ciência e a Tecnologia, Portugal
2010/06/28 - 2010/07/23 Developer and supervisor of UJr's Project: "Química: Uma Ciência sem Fronteiras", 2010 series of Universidade Júnior Universidade do Porto, Portugal
Projects

Grant

Designation Funders
2012/01/01 - 2015/12/31 Metals' Data for Biomolecular Force Fields
SFRH/ BD/78397/2011
PhD Student Fellow
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal
 Fundação para a Ciência e Tecnologia
Concluded

Contract

Designation Funders
2022/04/01 - Current Rational engineering of bacterial sulfur oxidoreductases for the capture and recycling of sulfur-based pollutants
2021.00391.CEECIND/CP1662/CT0003
Principal investigator
REQUIMTE LAQV Porto, 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
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.A2
Principal investigator
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
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
Principal investigator
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2023/03/08 - 2024/03/07 Murderous Venom- An Universal and Affordable Antidote Against Snakebite
EHPC-REG-2022R03-205
Co-Principal Investigator (Co-PI)
REQUIMTE LAQV Porto, Portugal

Universidade do Porto Faculdade de Ciências, Portugal
Partnership for Advanced Computing In Europe
Ongoing
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
Co-Principal Investigator (Co-PI)
REQUIMTE LAQV Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2019/04/01 - 2021/09/30 New Biocatalysts for Green Crude Oil Desulfurization
PTDC/QUI-QFI/28714/2017
REQUIMTE 2018-41
Post-doc
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2018/06/01 - 2021/05/31 Interdisciplinary in silico, organic synthesis, in vitro, and in vivo studies towards new anti-diabetic flavonoid scaffolds
PTDC/MED-QUI/29241/2017
Post-doc
Universidade de Aveiro, Portugal

Universidade do Porto, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
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
2017/01/01 - 2019/03/31 New Technologies for three Health Challenges of Modern Societies: Diabetes, Drug Abuse and Kidney Diseases
NORTE-01-0145-FEDER-000024
HEALTH_RL1_CI_GQC_01_3º
Post-doc
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Concluded
2016/05 - 2016/12 New Technologies for three Health Challenges of Modern Societies: Diabetes, Drug Abuse and Kidney Diseases
NORTE-01-0145-FEDER-000024
HEALTH_RL1_PHD_GQC_01_02
Post-doc Fellow
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Concluded

Other

Designation Funders
2020/04/01 - 2022/09/30 Biodegrading plastic
2019215204
Post-doc
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
 Partnership for Advanced Computing In Europe
Concluded
2019/03 - 2020/02 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
2019/03 - 2020/02 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 plastic
2010PA5065
Post-doc
Universidade do Porto Faculdade de Ciências, Portugal
 Partnership for Advanced Computing In Europe
Concluded
2017/05 - 2017/12 Assessment of natural compounds as novel anti-diabetic drugs
REQUIMTE/OPO-LIS/NFB2017
Post-doc
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal
 REQUIMTE Unidade de Ciências Biomoleculares Aplicadas
Concluded
Outputs

Publications

Book chapter
  1. Brás, N.F.; Coimbra, J.T.S.; Neves, Rui P. P.; Cerqueira, N.M.F.S.A.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. Corresponding author: Ramos, M.J.. "Computational Biochemistry". In Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. -: Elsevier, 2015.
    Published • 10.1016/b978-0-12-409547-2.10833-9
Conference abstract
  1. Makurat, Samanta; Chomicz-Manka, Lidia; Neves, Rui P. P.; Sousa, Sérgio F.; Fernandes, Pedro A.; Wityk, P.; Wieczór, M.; Czub, J.; Rak, Janusz. "QM/MM ONIOM calculations for DNA damage by solvated electrons. Optimizing a methodology for the modeling of radiotherapy-induced lesions". Paper presented in 3rd Congress of Polish Biosciences BIO 2018 – Through interdisciplinary approach into new solutions, Gdansk, 2018.
    Published
Conference poster
  1. Neves, Rui P. P.. "Towards new catalysts for sulfur capture, recycling and storage". Paper presented in 2023 EU US Frontiers of Engineering Symposium, 2023.
  2. Viegas, Matilde F.; Neves, Rui P. P.; Ramos, Maria J.; Fernandes, Pedro A.. "QM/MM study of the reaction mechanism of the extremozyme Glucuronoyl Esterase as a sustainable approach for Biofuel production". Paper presented in XXVI Encontro Nacional da Sociedade Portuguesa de Química, 2019.
  3. Neves, Rui P. P.. "Computational engineering of efficient enzyme catalysts for biodesulfurization of sour crude oil through 4S pathway". Paper presented in 10th Triennial Congress of the International Society for Theoretical Chemical Physics, 2019.
  4. Santos, Luciano E. R.; Neves, Rui P. P.. "Computational study of the reaction mechanism of the aromatic L-amino acid decarboxylase, an enzyme involved on the biosynthesis of serotonin and melatonin". Paper presented in 12th Meeting of Young Researchers of University of Porto (IJUP 2019), 2019.
  5. Amaral, Luísa M. P. F.; Neves, Rui P. P.; Videira, Romeu A.; Andrade, Paula B.; Valentão, Patrícia; Pereira, David P.; Ramos, Maria J.; Fernandes, Pedro A.. "Structure-based virtual screening approach to identify alpha-glucosidase inhibitors". Paper presented in XXIV Encontro Luso Galego de Química, 2018.
  6. Makurat, Samanta; Neves, Rui P. P.; Chomicz-Manka, Lidia; Sousa, Sérgio F.; Fernandes, Pedro A.; Wityk, P.; Wieczór, M.; Czub, J.; Rak, Janusz. "QM/MM ONIOM calculations for DNA damage by solvated electrons. Optimizing a methodology for the modeling of radiotherapy-induced lesions". Paper presented in 3rd Congress of Polish Biosciences BIO 2018 – Through interdisciplinary approach into new solutions, 2018.
  7. Medina, Fabiola E.; Neves, Rui P. P.; Ramos, Maria J.; Fernandes, Pedro A.. "A QM/MM study of the catalytic mechanism of human ß-ketoacyl reductase". Paper presented in 11th Triennial Congress of the World Association of Theoretical and Computational Chemists, 2017.
  8. Barbosa, Ana C. C.; Neves, Rui P. P.; Fernandes, Pedro A.; Ramos, Maria J.. "An Atomistic Study of the Catalytic Mechanism of Dibenzothiophene Monooxygenase DszC with QM/MM Calculations". Paper presented in 4th Meeting of Young Researchers in Structural Computational Biology, 2016.
  9. Barbosa, Ana C. C.; Neves, Rui P. P.; Fernades, Pedro A.; Ramos, Maria J.. "Reaction Mechanism of Dibenzothiophene Monooxygenase DszC using Quantum Mechanics/Molecular Mechanics Calculations". Paper presented in XIX Congress of the Portuguese Biochemical Society, 2016.
  10. Neves, Rui P. P.; Fernades, Pedro A.; Ramos, Maria J.. "QM/MM Study of the Enzymatic Mechanism of the Homo Sapiens Isocitrate Dehydrogenase". Paper presented in Binding free energy and kinetics: computation meets experiments, 2014.
  11. Neves, Rui P. P.; Sousa, Sérgio F.; Fernandes, Pedro A.; Ramos, Maria J.. "A Parameterization Scheme on Manganese Metalloproteins for Biomolecular Force-Fields". Paper presented in X GIRONA SEMINAR on Theoretical and Computational Chemistry for the Modeling of Biochemical Systems: From Theory to Applications, 2012.
  12. Neves, Rui P. P.; Sousa, Sérgio F.; Fernandes, Pedro A.; Ramos, Maria J.. "Setting a New Biomolecular Force-Field: Parameterizing Manganese First Coordination Spheres from Metalloproteins". Paper presented in 3rd Portuguese Young Chemists Meeting - 3PYCheM, 2012.
Journal article
  1. Makurat, Samanta; Neves, Rui P. P.; Ramos, Maria J.; Rak, Janusz. Corresponding author: Makurat, Samanta. "QM/MM MD Study on the Reaction Mechanism of Thymidine Phosphorylation Catalyzed by the Enzyme Thermotoga maritima Thymidine Kinase 1". ACS Catalysis 14 13 (2024): 9840-9849. http://dx.doi.org/10.1021/acscatal.4c01867.
    Open access • 10.1021/acscatal.4c01867
  2. Ferreira, Pedro; Neves, Rui P. P.; Miranda, Filipa P.; Cunha, Ana V.; Havenith, Remco W. A.; Ramos, Maria J.; Fernandes, Pedro A.. Corresponding author: Fernandes, Pedro A.. "DszA Catalyzes C–S Bond Cleavage through N5–Hydroperoxyl Formation". Journal of Chemical Information and Modeling 64 10 (2024): 4218-4230. http://dx.doi.org/10.1021/acs.jcim.4c00301.
    Open access • Published • 10.1021/acs.jcim.4c00301
  3. Jerves, Carola; Neves, Rui P. P.; da Silva, Saulo L.; Ramos, Maria J.; Fernandes, Pedro A.. Corresponding author: Fernandes, Pedro A.. "Rate-enhancing PETase mutations determined through DFT/MM molecular dynamics simulations". New Journal of Chemistry 48 1 (2024): 45-54. http://dx.doi.org/10.1039/d3nj04204a.
    Open access • Published • 10.1039/d3nj04204a
  4. Das, Sudip; Raucci, Umberto; Neves, Rui P. P.; Ramos, Maria J.; Parrinello, Michele. Corresponding author: Ramos, Maria J.. "How and When Does an Enzyme React? Unraveling a-Amylase Catalytic Activity with Enhanced Sampling Techniques". ACS Catalysis 13 12 (2023): 8092-8098. http://dx.doi.org/10.1021/acscatal.3c01473.
    Published • 10.1021/acscatal.3c01473
  5. Neves, Rui P. P.; Araújo, Bruno; Ramos, Maria J.; Fernandes, Pedro A.. Corresponding author: Fernandes, Pedro A.. "Feedback Inhibition of DszC, a Crucial Enzyme for Crude Oil Biodessulfurization". Catalysts 13 4 (2023): 736. http://dx.doi.org/10.3390/catal13040736.
    Open access • Published • 10.3390/catal13040736
  6. Neves, Rui P. P.; Ramos, Maria J.; Fernandes, Pedro A.. Corresponding author: Fernandes, Pedro A.. "Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis". Journal of Chemical Information and Modeling 63 1 (2022): 20-26. http://dx.doi.org/10.1021/acs.jcim.2c01337.
    Open access • Published • 10.1021/acs.jcim.2c01337
  7. Viegas, Matilde F.; Neves, Rui P. P.; Ramos, Maria J.; Fernandes, Pedro A.. Corresponding author: Fernandes, Pedro A.. "QM/MM Study of the Reaction Mechanism of Thermophilic Glucuronoyl Esterase for Biomass Treatment". ChemPhysChem 23 20 (2022): http://dx.doi.org/10.1002/cphc.202200269.
    Published • 10.1002/cphc.202200269
  8. Neves, Rui P. P.; Fernandes, Pedro A.; Ramos, Maria J.. Corresponding author: Neves, Rui P. P.. "Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by a-Amylase Explored with QM/MM Molecular Dynamics". Journal of Chemical Information and Modeling 62 15 (2022): 3638-3650. http://dx.doi.org/10.1021/acs.jcim.2c00691.
    Open access • Published • 10.1021/acs.jcim.2c00691
  9. Coimbra, João T. S.; Neves, Rui P. P.; Cunha, Ana V.; Ramos, Maria J.; Fernandes, Pedro A.. Corresponding author: Fernandes, Pedro A.. "Cover Feature: Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease (Chem. Eur. J. 42/2022)". Chemistry – A European Journal 28 42 (2022): http://dx.doi.org/10.1002/chem.202202001.
    Published • 10.1002/chem.202202001
  10. Coimbra, João TS; Neves, Rui P. P.; Cunha, Ana V.; Ramos, Maria Joao; Fernandes, Pedro Alexandrino. Corresponding author: Fernandes, Pedro Alexandrino. "Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease". Chemistry – A European Journal 28 42 (2022): http://dx.doi.org/10.1002/chem.202201066.
    Published • 10.1002/chem.202201066
  11. Neves, Rui P. P.; Cunha, Ana V.; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. Corresponding author: Ramos, Maria Joao. "Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms". ChemPhysChem 23 13 (2022): http://dx.doi.org/10.1002/cphc.202200159.
    Published • 10.1002/cphc.202200159
  12. Carola Jerves; Rui P. P. Neves; Maria J. Ramos; Saulo da Silva; Pedro A. Fernandes. "Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations". ACS Catalysis (2021): 11626-11638. https://doi.org/10.1021/acscatal.1c03700.
    10.1021/acscatal.1c03700
  13. Neves, Rui P. P.; Ferreira, Pedro; Medina, Fabiola E.; Paiva, Pedro; Sousa, João P. M.; Viegas, Matilde F.; Fernandes, Pedro A.; Ramos, Maria J.. Corresponding author: Ramos, Maria J.. "Engineering of PKS Megaenzymes—A Promising Way to Biosynthesize High-Value Active Molecules". Topics in Catalysis 65 1-4 (2021): 544-562. http://dx.doi.org/10.1007/s11244-021-01490-5.
    Published • 10.1007/s11244-021-01490-5
  14. Pinto, Alexandre V.; Ferreira, Pedro; Neves, Rui P. P.; Fernandes, Pedro A.; Ramos, Maria J.; Magalhães, Alexandre L.. Corresponding author: Ramos, Maria J.. "Reaction Mechanism of MHETase, a PET Degrading Enzyme". ACS Catalysis 11 16 (2021): 10416-10428. http://dx.doi.org/10.1021/acscatal.1c02444.
    Published • 10.1021/acscatal.1c02444
  15. Neves, Rui P. P.; Paiva, Pedro (A319-EC13-BE88); Medina, Fabiola E; Viegas, Matilde F.; Ferreira, Pedro; Sousa, João P. M.; Ramos, Maria Joao; Fernandes, Pedro Alexandrino. Corresponding author: Fernandes, Pedro Alexandrino. "Animal Fatty Acid Synthase: A Chemical Nanofactory". Chemical Reviews 121 15 (2021): 9502-9553. http://dx.doi.org/10.1021/acs.chemrev.1c00147.
    Published • 10.1021/acs.chemrev.1c00147
  16. Brás, Natércia F.; Neves, Rui P.P.; Lopes, Filipa A.A.; Correia, Márcia A.S.; Palma, Angelina S.; Sousa, Sérgio F.; Ramos, Maria J.. Corresponding author: Brás, Natércia F.. "Combined in silico and in vitro studies to identify novel antidiabetic flavonoids targeting glycogen phosphorylase". Bioorganic Chemistry (2020): 104552. http://dx.doi.org/10.1016/j.bioorg.2020.104552.
    Published • 10.1016/j.bioorg.2020.104552
  17. Neves, Rui P. P.; Sousa, João (9A1A-538A-FB44); Ferreira, Pedro; Ramos, Maria Joao; Fernandes, Pedro Alexandrino. Corresponding author: Fernandes, Pedro Alexandrino. "The bacterial 4S pathway - an economical alternative for crude oil desulphurization that reduces CO2 emissions". Green Chemistry 22 22 (2020): 7604-7621. http://dx.doi.org/10.1039/d0gc02055a.
    Published • 10.1039/d0gc02055a
  18. Sousa, João P. M.; Neves, Rui P. P.; Sousa, Sérgio F.; Ramos, Maria J.; Fernandes, Pedro A.. Corresponding author: Fernandes, Pedro A.. "Reaction Mechanism and Determinants for Efficient Catalysis by DszB, a Key Enzyme for Crude Oil Bio-desulfurization". ACS Catalysis 10 16 (2020): 9545-9554. http://dx.doi.org/10.1021/acscatal.0c03122.
    Published • 10.1021/acscatal.0c03122
  19. Goossens, Kenneth; Neves, Rui P. P.; Fernandes, Pedro Alexandrino; De Winter, Hans. Corresponding author: De Winter, Hans. "A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes". Journal of Chemical Information and Modeling 60 11 (2020): 5513-5528. http://dx.doi.org/10.1021/acs.jcim.0c00377.
    Published • 10.1021/acs.jcim.0c00377
  20. Pinto, Alexandre V. Pinto; Oliveira, Ana N. L. Oliveira; Jerves, Carola Jerves; Mendonça, Filipa Lopes de Mendonça; Coutinho, Inês F. M. Coutinho; Coimbra, João T. S. Coimbra; Sousa, João P.M. Sousa; et al. "Proteínas Virais no Protein Data Bank". Revista de Ciência Elementar 8 2 (2020): http://dx.doi.org/10.24927/rce2020.022.
    Open access • Published • 10.24927/rce2020.022
  21. Sousa, Sérgio F.; Neves, Rui P.P.; Waheed, Sodiq O.; Fernandes, Pedro A.; Ramos, Maria João. Corresponding author: Ramos, Maria João. "Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins". Biological Chemistry 400 5 (2019): 575-587. http://dx.doi.org/10.1515/hsz-2018-0319.
    Open access • Published • 10.1515/hsz-2018-0319
  22. Medina, Fabiola E.; Neves, Rui P. P.; Ramos, Maria J.; Fernandes, Pedro A.. Corresponding author: Fernandes, Pedro A.. "QM/MM Study of the Reaction Mechanism of the Dehydratase Domain from Mammalian Fatty Acid Synthase". ACS Catalysis 8 11 (2018): 10267-10278. http://dx.doi.org/10.1021/acscatal.8b02616.
    Published • 10.1021/acscatal.8b02616
  23. Barbosa, Ana C. C.; Neves, Rui P. P.; Sousa, Sérgio F.; Ramos, Maria Joao; Fernandes, Pedro Alexandrino. Corresponding author: Fernandes, Pedro Alexandrino. "Mechanistic Studies of a Flavin Monooxygenase: Sulfur Oxidation of Dibenzothiophenes by DszC". ACS Catalysis 8 10 (2018): 9298-9311. http://dx.doi.org/10.1021/acscatal.8b01877.
    Published • 10.1021/acscatal.8b01877
  24. Viegas, Matilde F.; Neves, Rui P. P.; Ramos, Maria Joao; Fernandes, Pedro Alexandrino. Corresponding author: Fernandes, Pedro Alexandrino. "Modeling of Human Fatty Acid Synthase and in Silico Docking of Acyl Carrier Protein Domain and Its Partner Catalytic Domains". The Journal of Physical Chemistry B 122 1 (2018): 77-85. http://dx.doi.org/10.1021/acs.jpcb.7b09645.
    Published • 10.1021/acs.jpcb.7b09645
  25. Simões, Inês C. M.; Coimbra, João T. S.; Neves, Rui P. P.; Costa, Inês P. D.; Ramos, Maria J.; Fernandes, Pedro A.. Corresponding author: Fernandes, Pedro A.. "Properties that rank protein:protein docking poses with high accuracy". Physical Chemistry Chemical Physics 20 32 (2018): 20927-20942. http://dx.doi.org/10.1039/c8cp03888k.
    Published • 10.1039/c8cp03888k
  26. Neves, Rui P. P.; Fernandes, Pedro A.; Ramos, Maria J.. Corresponding author: Ramos, Maria J.. "Mechanistic insights on the reduction of glutathione disulfide by protein disulfide isomerase". Proceedings of the National Academy of Sciences 114 24 (2017): E4724-E4733. http://dx.doi.org/10.1073/pnas.1618985114.
    Open access • Published • 10.1073/pnas.1618985114
  27. Medina, Fabiola E.; Neves, Rui P. P.; Ramos, Maria J.; Fernandes, Pedro A.. Corresponding author: Fernandes, Pedro A.. "A QM/MM study of the reaction mechanism of human ß-ketoacyl reductase". Physical Chemistry Chemical Physics 19 1 (2017): 347-355. http://dx.doi.org/10.1039/c6cp07014k.
    Published • 10.1039/c6cp07014k
  28. Sousa, Sérgio F.; Ribeiro, António J. M.; Neves, Rui P. P.; Brás, Natércia F.; Cerqueira, Nuno M. F. S. A.; Fernandes, Pedro A.; Ramos, Maria J.. Corresponding author: Ramos, Maria J.. "Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms". Wiley Interdisciplinary Reviews: Computational Molecular Science 7 2 (2016): e1281. http://dx.doi.org/10.1002/wcms.1281.
    Open access • Published • 10.1002/wcms.1281
  29. Sousa, Sérgio F.; Sousa, Joana F. M.; Barbosa, Ana C. C.; Ferreira, Cleide E.; Neves, Rui P. P.; Ribeiro, António J. M.; Fernandes, Pedro A.; Ramos, Maria J.. Corresponding author: Ramos, Maria J.. "Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)". The Journal of Physical Chemistry A 120 27 (2016): 5300-5306. http://dx.doi.org/10.1021/acs.jpca.6b01536.
    Published • 10.1021/acs.jpca.6b01536
  30. Neves, Rui P. P.; Fernandes, Pedro A.; Ramos, Maria J.. Corresponding author: Ramos, Maria J.. "Unveiling the Catalytic Mechanism of NADP+-Dependent Isocitrate Dehydrogenase with QM/MM Calculations". ACS Catalysis 6 1 (2015): 357-368. http://dx.doi.org/10.1021/acscatal.5b01928.
    Published • 10.1021/acscatal.5b01928
  31. Coimbra, João T.S.; Neves, Rui P. P.; Passos, Óscar; Jarukanont, Daungruthai; Fernandes, Pedro A.; Patel, Shekhar; Garcia, Martin E.; Ramos, Maria J.. Corresponding author: Ramos, Maria J.. "Influence of the environment on protein bond energies". Chemical Physics Letters 615 (2014): 75-82. http://dx.doi.org/10.1016/j.cplett.2014.09.066.
    Published • 10.1016/j.cplett.2014.09.066
  32. Neves, Rui P. P.; Fernandes, Pedro A.; Varandas, António J. C.; Ramos, Maria J.. Corresponding author: Ramos, Maria J.. "Benchmarking of Density Functionals for the Accurate Description of Thiol–Disulfide Exchange". Journal of Chemical Theory and Computation 10 11 (2014): 4842-4856. http://dx.doi.org/10.1021/ct500840f.
    Published • 10.1021/ct500840f
  33. Neves, Rui P. P.; Sousa, Sérgio F.; Fernandes, Pedro A.; Ramos, Maria J.. Corresponding author: Ramos, Maria J.. "Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins". Journal of Chemical Theory and Computation 9 6 (2013): 2718-2732. http://dx.doi.org/10.1021/ct400055v.
    Published • 10.1021/ct400055v
  34. Sousa, Sérgio F.; Ribeiro, António J. M.; Coimbra, João T. S.; Neves, Rui P. P.; Martins, Sílvia A.; Moorthy, N.S.H.N.; Fernandes, Pedro A.; Ramos, Maria J.. Corresponding author: Ramos, Maria 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://dx.doi.org/10.2174/0929867311320180002.
    Published • 10.2174/0929867311320180002
Thesis / Dissertation
  1. Rui Pedro Pimenta Das Neves. "Metals'Data for Biomolecular Force Fields". PhD, Universidade do Porto, 2016. http://hdl.handle.net/10216/92819.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2019/12/02 Unveiling enzyme reaction mechanisms as means to develop sustainable industrial processes 3rd International Caparica Christmas Conference on Translational Chemistry 2019
PROTEOMASS BIOSCOPE Team (Costa da Caparica, Portugal)
2019/10/11 Can machine-learning boost enzyme-directed rational drug-design? I Biomedical Engineering Summit
Associação Nacional de Estudantes de Engenharia Biomédica (Lisbon, Portugal)
2019/09 Computational Biochemistry and Enzyme Reaction Mechanisms Master course of Computational Biochemistry (Q4003)
University of Porto Faculty of Sciences (Porto, Portugal)
2019/05/05 Enzyme reaction mechanisms Master course of Bioinformatics (Q4025)
University of Porto Faculty of Sciences (Porto, Portugal)
2019/02/27 Can enzyme reaction mechanisms solve real world problems? Talks of the Department of Chemistry and Biochemistry
University of Porto Faculty of Sciences (Porto, Portugal)
2018/10/11 Kinetic and Thermodynamic Characterization of Thiol-Disulfide Exchange: From Small Molecules to Molecular Machines 44th International Congress of Theoretical Chemists of Latin Expression (QUITEL 2018)
Centro de Extensión UC Pontificia Universidad Católica de Chile (Santiago de Chile, Chile)
2018/09/28 Assessment and optimization of antidiabetic compounds through computational and experimental approaches UCIBIO Annual Meeting 2018
NOVA University of Lisbon Faculty of Sciences and Technology (Lisboa, Portugal)
2018/04/19 In silico search of novel compounds for the treatment of diabetes Master course of Bioinformatics (Q4025)
University of Porto Faculty of Sciences (Porto, Portugal)
2017/06/26 Atomistic Study of Enzyme Reaction Mechanisms through Computational Methods 1st Meeting of Researchers from the Chemistry and Biochemistry Department
University of Porto Faculty of Sciences (Porto, Portugal)
2017/04/04 Determination of Thermodynamic Quantities from MD simulations Undergraduate course of Molelcular Simulation (Q3023)
University of Porto Faculty of Sciences (Porto, Portugal)
2015/04/27 MD simulations to model Protein:Protein complexes Undergraduate course of Computational Biological Chemistry (Q254)
University of Porto Faculty of Sciences (Porto, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2020/09/01 - 2021/11/11 Enzymatic Technologies for Cleaning Petroleum with Low CO2 Emissions
Co-supervisor
 Biochemistry (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2019/02/01 - 2019/07 Computational study of L-aromatic amino acid decarboxylase , an enzyme involved in the synthesis of the sleep-regulation hormone melatonin
Supervisor
 Biochemistry (Degree)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, 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)
 University of Porto - Casa Comum, 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 9ª Edição do Encontro de Investigação Jovem da Universidade do Porto (IJUP) (2016/02/17 - 2016/02/19)
Meeting (Other)
 Universidade do Porto, Portugal
2015/05/13 - 2015/05/15 8ª Edição do Encontro de Investigação Jovem da Universidade do Porto (IJUP) (2015/05/13 - 2015/05/15)
Meeting (Other)
 Universidade do Porto, Portugal
2012/05/04 - 2012/05/08 COnvergent Distributed Environment for Computational Spectroscopy – European Cooperation in Science and Technology (CoDECS-COST) Workshop (2012/05/04 - 2012/05/08)
Workshop (Member of the Organising Committee)
 Universidade do Porto Faculdade de Ciências, Portugal
2010 - 2010/07/23 Developer and supervisor of UJr Project: Química: Uma Ciência sem Fronteiras (2010/06/28 - 2010/07/23)
Other (Other)
 Universidade do Porto, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2023/10/15 - 2023/10/18 Invited general participant in the symposium US-EU Frontiers of Engineering 2023, to discuss cutting-edge developments in four areas: The Quantum Era Challenge, Computational Era in Life Sciences and chemistry, Green Hydrogen and Future Directions in Additive Manufacturing.
Symposium
 US-EU Frontiers of Engineering 2023
National Academy of Engineering, United States

European Council of Applied Sciences, Technologies and Engineering, France

Slovenian Academy of Engineering , Slovenia
2021/09/30 - 2021/10/01 Participant in the 2nd TIMB3 Symposium entitled: "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 Participant in the Virtual Workshop entitled "Computer Simulation and Theory of Macromolecules"
Workshop
 Hünfeld 2021: Computer Simulation and Theory of Macromolecules
Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Germany
2017/07/09 - 2017/07/14 Supervisor in the "School of Chemistry and Biochemistry"
Other
 School of Chemistry and Biochemistry
Universidade do Porto Faculdade de Ciências, Portugal
2017/07/12 - 2017/07/12 Participant in the "Workshop on Innovation and Intelectual Property"
Workshop
 Workshop on Innovation and Intelectual Property
REQUIMTE, Portugal
2015/07/06 - 2015/07/10 Supervisor in the "School of Chemistry and Biochemistry"
Other
 School of Chemistry and Biochemistry
Universidade do Porto Faculdade de Ciências, Portugal
2014/05/21 - 2014/05/23 Attendant in the "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
2013/03/14 - 2013/03/17 Participant in the "Science, Teaching and Innovation Fair of University of Porto"
Exhibition
 Science, Teaching and Innovation Fair of University of Porto
Universidade do Porto, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2024/01/22 Enzymatic Synthesis of Amphiphilic Polymer-drug Conjugates for Cancer Treatment
(Thesis) Main arguer
 Pedro Miguel Reis Figueiredo (PhD)
Universidade de Coimbra Instituto de Investigação Interdisciplinar, Portugal
2023/09/19 Multiscalar strategies for the characterization of engineered P450 enzymes
(Thesis) Main arguer
 Jordi Soler i Parpal (PhD)
Universitat de Girona, Spain

Universitat de Girona Institut de Quimica Computacional i Catalisi, Spain
2018/10/01 QM/MM Study of DszB Reaction Mechanism for Crude Oil Biodesulphurization
(Thesis) Main arguer
 João Pedro Marques de Sousa (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2023 - Current Journal of Biomolecular Structure and Dynamics (1538-0254) Taylor & Francis Inc
2023 - Current Journal of Chemical Technology and Biotechnology (0268-2575) John Wiley and Sons Ltd
2022 - Current RSC Advances (2046-2069) Royal Society of Chemistry
2021 - Current Proteins: Structure, Function and Bioinformatics (1097-0134) Wiley-Liss Inc.
2019/01 - Current ACS Catalysis (2155-5435) American Chemical Society
2019/07 - 2019/09 The Journal of Physical Chemistry (1541-5740) American Chemical Society
2018/12 - 2019/01 Journal of Chemical Information and Modeling (1549-960X) American Chemical Society
2018/08/16 - 2018/09/05 Chemistry - A European Journal (1521-3765) Wiley (John Wiley & Sons)

Mentoring / Tutoring

Topic Student name
2022/10/01 - Current Development of new chiral stationary phases for liquid chromatography based on xanthone and polysaccharide derivatives by a rational approach Rita Alexandra Ferreira Alves de Lima
2022/06/01 - Current Computational study of the PET-degrading PE-H enzyme with QM/MM simulations Samah Nassir
2024/02/12 - 2024/05/28 Modeling the interaction and the reaction mechanism of quinone reduction by bacterial sulfide:quinone reductase Ana Luísa de Sousa Rocha
2019/10 - 2022/09 Computational Study of the Hydrolysis of PET catalysed by the enzyme PETase Fanny Carola Jerves Vázquez
2020/09/01 - 2021/11/11 Enzymatic Technologies for Cleaning Petroleum with Low CO2 Emissions Filipa Pinto de Barros Miranda
2019/01 - 2021/05/19 Understanding and Optimizing Extremozymes for Industrial Processes Matilde Freitas Viegas
2019/09 - 2019/12 Development of novel bacterial transglycosylase inhibitors through computational chemistry Kenneth Goossens
2015/04 - 2018 Fatty acid synthase enzyme - Catalytic mechanisms, Fabiola Medina
2017/09 - 2017/12 Modified nucleosides as nucleoside kinases substrates. QM/MM studies on enzymatic activity Samanta Makurat
2016/09 - 2017/07 QM/MM study of the reaction mechanism of glutredoxin Sodiq Waheed
2015/08 - 2016/12/31 Reaction Mechanism of the oxidation of DBT by DszC studied by QM/MM calculations Ana Catarina Barbosa
2016/09 - 2016/12 Computational Studies of the Mechanisms of Catalysis and Inhibition of Cysteine Proteases Kemel Arafet
2016/02 - 2016/05 Rational design of tubulin binding agents with potential anticarcinogenic action Matías Zuñiga
2015/09 - 2015/12 Computational studies on cytochrome P450 Elisa Bernes
2014/01 - 2014/07 Estudo computacional da estabilidade de carbocatiões com métodos ab Initio Maria Madalena Silva, Nádia Figueiredo, Olívia de Castro
Distinctions

Award

2008 Prémio Doutor Mendonça Monteiro
Universidade do Porto Faculdade de Ciências, Portugal

Other distinction

2011 PhD grant SFRH/BD/78397/2011
Fundação para a Ciência e a Tecnologia, Portugal
2007 Bolsa de mérito referente ao ano letivo 2006/2007
Universidade do Porto Faculdade de Ciências, Portugal