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Sérgio Filipe Sousa graduated in Chemistry (FCUP) in 2003 with first-class honors and completed a PhD in Computational Chemistry (FCUP, 2007), before pursuing a Post-Doc on biomembrane simulations (2008). From 2008-2017 worked as Assistant Researcher in the Theoretical Chemistry group (FCUP-REQUIMTE), and as FCT Researcher (IF) since 2015. In late 2018, he moved to FMUP and created the BioSIM group (www.biosim.pt), which presently comprises 18 people. Published 142 papers in peer-reviewed journals, 11 book chapters and 14 proceedings. These articles account > 4450 citations, an h-index of 30 and an average number of citations of 30. Received the academic awards Eng Antonio de Almeida and Dr Mendonca Monteiro. Was awarded the "Premio Estimulo a Investigacao Gulbenkian 2009". Was the principal investigator (PI) of four projects funded by FCT, and was awarded an FCT starting grant (IF2014) and a very competitive FCT CEEC Individual Research Grant (CEEC2020 - Level 2). He presently collaborated in 12 other FCT projects as team member. Has been involved in teaching activities as Lecturer and Professor Auxiliar Convidado at Univ. of Porto (2007- 2018) and Univ. Católica Portuguesa (2009-2010), in several courses on the field of Bioinformatics and Computational Biochemistry (FCUP: B.Sc. and M.Sc. in Chemistry, Biochemistry and Bioinformatics; UCatolica: B.Sc. in Bioinformatics) and Escola Superior de Saúde (Lic Biotecnologia Medicinal; Msc Bioquímica da Saúde). Was an invited lecturer in several editions of the European Master in Theoretical Chemistry and Computational Modeling (2010, 2011, 2014 and 2017). He is a member of the editorial board of 4 journals and is guest editing 5 special issues. He has supervised 5 PhD students as supervisor/co-supervisor, > 13 M.Sc students, and > 15 undergraduates. Presently, he is the supervisor or co-supervisor of 11 Ph.D. students and 6 M.Sc. Students. He reviewed articles for ca. 72 different journals (total of 293 confirmed reviews in publons, including 172 revisions just in 2020-2022) and acted as handling editor for 57 articles (source publons). He also participated as an evaluator in project calls for NSF (USA), ANR (France), and ANPCyT (Argentina), NSC (Poland), Slovenia and EU. In addition, he participated as main examiner in the juris of 6 PhD Thesis, 5 MSc Thesis and 8 graduation projects discussions. Organized several scientific events and headed the organization of the EJIBCE2018 (December 2018, FMUP). He is member of the scientific committee of the IJUP ¿ Encontro de Investigação Jovem da Univ Porto (2019-2024), acting as the representative for Chemistry. In 2022, he was listed among the world's top 2% most cited researchers by the Stanford University Ranking. 
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Identificação

Identificação pessoal

Nome completo
Sérgio Filipe Maia de Sousa

Nomes de citação

  • Sousa, Sérgio F.

Identificadores de autor

Ciência ID
2D13-FC03-3173
ORCID iD
0000-0002-6560-5284
Researcher Id
A-5062-2008
Scopus Author Id
35300847400

Endereços de correio eletrónico

  • sergiofsousa@med.up.pt (Profissional)

Moradas

  • BioSIM - LAQV/REQUIMTE, BioSIM - Departamento de BioMedicina Faculdade de Medicina da Universidade do Porto Alameda Prof. Hernâni Monteiro, 4200-319 Porto Portugal, 4169-007 , Porto, Porto, Portugal (Profissional)

Websites

Domínios de atuação

  • Ciências Exatas - Química
  • Ciências Naturais - Ciências Biológicas - Bioquímica
  • Ciências Exatas - Ciências da Computação e da Informação - Bioinformática

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Inglês Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Francês Utilizador elementar (A1) Utilizador independente (B1) Utilizador elementar (A1) Utilizador elementar (A1)
Alemão Utilizador independente (B1) Utilizador independente (B1) Utilizador independente (B1) Utilizador independente (B1)
Espanhol; Castelhano Utilizador elementar (A1) Utilizador independente (B1) Utilizador elementar (A1) Utilizador elementar (A1)
Formação
Grau Classificação
2008
Concluído
 Pos Doutoramento (Pós-doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
"Drug Permeation through Biomembranes" (TESE/DISSERTAÇÃO)
 n/a
2007
Concluído
 Química (Doutoramento)
Especialização em Sem especialidade
Universidade do Porto Faculdade de Ciências, Portugal
"Theoretical Studies on the Catalytic and Inhibition Mechanisms of the Farnesyltransferase Enzyme" (TESE/DISSERTAÇÃO)
2003
Concluído
 Licenciatura em Química (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal
"Theoretical Studies on Cythocromes P450" (TESE/DISSERTAÇÃO)
 16
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2015 - 2021/02/28 Investigador Auxiliar (carreira) (Investigação) REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal
2014/05/01 - 2014/12/31 Pós-doutorado (Investigação) REQUIMTE, Departamento de Química e Bioquimica, Faculdade de Ciências, Universidade do Porto, Portugal
2008/05/01 - 2014/04/30 Investigador Auxiliar (carreira) (Investigação) Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
2007/11/01 - 2008/04/30 Pós-doutorado (Investigação) Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento 		Empregador
2018/01/01 - 2018/07/01 Professor Auxiliar Convidado (Docente Universitário) Universidade do Porto Faculdade de Ciências, Portugal
2009/01/01 - 2010/07/01 Professor Auxiliar Convidado (Docente Universitário) Universidade Católica Portuguesa Escola Superior de Biotecnologia, Portugal
2009/01/01 - 2010/06/01 Professor Auxiliar Convidado (Docente Universitário) Universidade do Porto Faculdade de Ciências, Portugal

Outros

Categoria Profissional
Instituição de acolhimento 		Empregador
2021/03/01 - Atual CEEC 2020 - Investigador Auxiliar (Ref 2020.01423.CEECIND) LAQV/REQUIMTE - Faculdade de Medicina, Universidade do Porto, Portugal
LAQV/REQUIMTE - Faculdade de Medicina, Universidade do Porto, Portugal
2018 - Atual Group Leader - BioSIM LAQV/REQUIMTE - Faculdade de Medicina, Universidade do Porto, Portugal
2014/12/31 - Atual FCT Researcher IF2014 UCIBIO@REQUIMTE, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Portugal
2015/01/01 - 2019/12/31 Investigador FCT REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal
2008/05/01 - 2014/12/31 Associate Researcher (Investigador Auxiliar) REQUIMTE, Departamento de Química e Bioquimica, Faculdade de Ciências, Universidade do Porto, Portugal
2003/10/01 - 2007/10/30 PhD Student REQUIMTE, Departamento de Química e Bioquimica, Faculdade de Ciências, Universidade do Porto, Portugal
Projetos

Bolsa

Designação Financiadores
2021/01 - Atual Application of Molecular Dynamics Simulations in the Study of Biomolecular Interactions for the Identification of New Drug Candidates
CPCA/A00/7145/2020
CPCA/A00/7145/2020
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.

Fundação para a Ciência e a Tecnologia
Concluído
2021 - Atual Application of QM/MM Methods in the Development of Biocatalysts
CPCA/A00/7140/2020
CPCA/A00/7140/2020
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.

Fundação para a Ciência e a Tecnologia
Concluído
2024/01/01 - 2027/12/31 Simulations for aptamer design (AptaSims)
359266
Investigador
Suomen Akatemia
Em curso
2021/01/01 - 2025/12/31 Instituto para a Saúde e a Bioeconomia - Institute for Health and Bioeconomy
LA/P/0140/2020
Investigador
Fundação para a Ciência e a Tecnologia
Em curso
2023/01/01 - 2024/06/30 Engaging Libraries of Promising Oxindoles as Tyrosine-Kinase InhibitorS in Cancer Target Therapy
2022.02910.PTDC
Investigador
Fundação para a Ciência e a Tecnologia
Em curso
2022/06/01 - 2024/03/31 Refining Antimicrobial Peptides with cutting-edge strategies to tackle infections by Nontuberculous Mycobacteria
PTDC/BIA-MIC/3458/2020
Investigador
Fundação para a Ciência e a Tecnologia
Em curso
2021/04 - 2024/03 Otimizar Péptidos Antimicrobianos usando estratégias de ponta para combater infeções causadas por micobactérias não-tuberculosas
Provided by PTCRIS: PTDC/BIA-MIC/3458/2020
 Fundação para a Ciência e a Tecnologia
2020/01/01 - 2023/12/31 Unidade de Ciências Biomoleculares Aplicadas - Applied Molecular Biosciences Unit
UIDP/04378/2020
UIDB/04378/2020
Investigador
Fundação para a Ciência e a Tecnologia
Em curso
2022/03/01 - 2023 Optimization of Validated SARS-CoV-2 Antivirals against the New Emerging Variants
2021.09752.CPCA
Investigador responsável
Fundação para a Ciência e a Tecnologia
Em curso
2022/03/01 - 2023 Understanding non-B mTDNA Conformations using Molecular Dynamics Simulations
2021.09782.CPCA
Investigador
Fundação para a Ciência e a Tecnologia
Em curso
2022/02/01 - 2023 Cutting-edge QM/MM MD implementation for the study of enzymatic mechanisms
CPCA/A1/422043/2021
CPCA/A1/422043/2021
Co-Principal Investigator
Fundação para a Ciência e a Tecnologia

Fundação para a Ciência e a Tecnologia, I.P.
Em curso
2018/10 - 2022 New Biocatalysts for Green Crude Oil Desulfurization
PTDC/QUI-QFI/28714/2017
 Fundação para a Ciência e a Tecnologia
Concluído
2018/07 - 2022 Biopesticides and Food Preservatives from Nanoencapsulated Plant Extracts: Biological Evaluation, Molecular Modelling and Synthesis
PTDC/ASP-AGR/30154/2017
 Fundação para a Ciência e a Tecnologia
Concluído
2018/07 - 2022 RDB-TS - A reaction database for transition state information from quantum chemical calculation
NORTE-01-0145-FEDER-031689
 Fundação para a Ciência e a Tecnologia
Concluído
2018/07 - 2022 Dipeptide Crystals as Biomaterials for Gas Purification
PTDC/QUI-QFI/29914/2017
 Fundação para a Ciência e a Tecnologia
Concluído
2017 - 2019 Assessment of natural compounds as novel anti-diabetic drugs
UID/Multi/04378/2019
 REQUIMTE
2016 - 2019 New Technologies for three Health Challenges of Modern Societies: Diabetes, Drug Abuse and Kidney Diseases.
NORTE-01-0145-FEDER-00002
Investigador
CCDRN
Concluído
2013/01 - 2015/12 ENZYMATIC CATALYSIS - seeking a global picture
128544
Provided by PTCRIS: 128544
 Fundação para a Ciência e a Tecnologia, I.P.
2012/08 - 2015/08 New drugs to prevent Herpes Simplex virus type 1 infections
122916
Provided by PTCRIS: 122916
 Fundação para a Ciência e a Tecnologia, I.P.
2014/03 - 2015/02 Consensus Scoring - An Innovative Method to Find Leads for the Pharmaceutical Industry
Provided by PTCRIS: 134150
134150
 Fundação para a Ciência e a Tecnologia, I.P.
2010/06 - 2013/09 New Biomolecular Force Field
Provided by PTCRIS: 103118
103118
 Fundação para a Ciência e a Tecnologia, I.P.
2010/06 - 2013/05 An innovative methodology to calculate drug-receptor binding free energies
100372
Provided by PTCRIS: 100372
 Fundação para a Ciência e a Tecnologia, I.P.
2003/10 - 2007/09 STUDY OF CATALYTIC MECHANISM AND INHIBITION OF THE PROTEIN FARNESYLTRANSFERASE
Provided by PTCRIS: SFRH/BD/12848/2003
 Fundação para a Ciência e a Tecnologia, I.P.

Projeto

Designação Financiadores
2021/03/01 - Atual CEEC2020 - Development of Biocatalysts for Industrial Applications: From plastic degradation to the pharmaceutical chemistry
2020.01423.CEECIND
CEEC2020 Researcher
UCIBIO@REQUIMTE, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2021/01/01 - 2025/12/31 Institute for Health and Bioeconomy
10.54499/LA/P/0140/2020
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Universidade do Porto, Portugal

Universidade Nova de Lisboa, Portugal

Unidade de Ciências Biomoleculares Aplicadas, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

INESC Microsistemas e Nanotecnologias, Portugal

Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2018/07/01 - 2022/06/30 RDB-TS: Uma base de dados de reações químicas baseadas em informação de estados de transição derivados de cálculos quânticos.
PTDC/QUI-QFI/31689/2017
Universidade do Minho, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2014 - 2015 Consensus Scoring – A new methodology to identify lead compounds for the pharmaceutical industry
EXPL/QEQ-COM/1125/2013
EXPL/QEQ-COM/1125/2013
Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2011/01/01 - 2012/12/31 Strategic Project - LA 6 - 2011-2012
PEst-C/EQB/LA0006/2011
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
Produções

Publicações

Artigo em conferência
  1. José Ricardo A. Coelho; Tatiana F. Vieira; Renato B. Pereira; David M. Pereira; Elisabete M. S. Castanheira; António Gil Fortes; Sérgio F. Sousa; Maria José G. Fernandes; Maria Sameiro T. Gonçalves. "Synthesis, Insecticidal Activity and Computational Studies of Eugenol-Based Insecticides". 2022.
    10.3390/ecsoc-26-13649
  2. Miguel A. F. Ribeiro; Tatiana F. Vieira; Maria José G. Fernandes; Renato B. Pereira; David M. Pereira; Elisabete M. S. Castanheira; A. Gil Fortes; Sérgio F. Sousa; M. Sameiro T. Gonçalves. "Synthesis and In Silico Evaluation of Potential Insecticide Activity of Benzamides". 2021.
    10.3390/ecsoc-25-11770
  3. Tatiana Vieira; Rita Magalhães; Sérgio F. Sousa. "Development and Validation of a Multi-Level Computational Protocol for Drug Repurposing in the Treatment of Bacterial Infections". 2021.
    10.3390/ecsoc-25-11728
  4. José R. A. Coelho; Tatiana F. Vieira; Renato B. Pereira; David M. Pereira; Elisabete M. S. Castanheira; A. Gil Fortes; Sérgio F. Sousa; Maria José G. Fernandes; M. Sameiro T. Gonçalves. "Eugenol Ester Derivatives: Synthesis, Insecticidal Activity and Computational Studies". 2021.
    10.3390/ecsoc-25-11787
  5. Sousa, Sérgio F.; Silva Teixeira, C.S.; Sousa, S.F.; Cerqueira, N.M.F.S.A.. "Molecular dynamic simulations and QM/MM studies addressed to build an active Tryptophan Synthase model. A critical enzyme to treat tuberculosis". 2019.
    10.1109/enbeng.2019.8692492
  6. Fernandes, P. A.; Sousa, Sérgio F.; Cerqueira, N.M.F.S.A.; Ramos, M. J.. "What a Computer can do in Biological Chemistry?". Trabalho apresentado em Proceedings of the 2nd European Conference on Chemistry for Life Sciences, Wroclaw, 2007.
Artigo em revista
  1. Fernandes, Susana; Sousa, Mariana; Martins, Fábio G.; Simões, Manuel; Sousa, Sérgio F.. "Protocol for in silico characterization of natural-based molecules as quorum-sensing inhibitors". STAR Protocols 5 4 (2024): 103367. http://dx.doi.org/10.1016/j.xpro.2024.103367.
    10.1016/j.xpro.2024.103367
  2. Paquete-Ferreira, João; Freire, Filipe; Fernandes, Henrique S.; Muthukumaran, Jayaraman; Ramos, João; Bryton, Joana; Panjkovich, Alejandro; et al. "Structural insights of an LCP protein–LytR–from Streptococcus dysgalactiae subs. dysgalactiae through biophysical and in silico methods". Frontiers in Chemistry 12 (2024): 1379914.. http://dx.doi.org/10.3389/fchem.2024.1379914.
    Publicado • 10.3389/fchem.2024.1379914
  3. Mendes, Filipa; Cátia Santos-Pereira; Vieira, Tatiana F.; Martins Pinto, Mélanie; Castro, Bruno B.; Sousa, Sérgio F.; Sousa, Maria João; Devin, Anne; Chaves, Susana R.. "The fungicide cymoxanil impairs respiration in Saccharomyces cerevisiae via cytochrome c oxidase inhibition". FEBS Letters (2024): http://dx.doi.org/10.1002/1873-3468.14907.
    10.1002/1873-3468.14907
  4. Sousa, Joana; Cátia Santos-Pereira; Gomes, Joana S.; Costa, Ângela M. A.; Santos, Andréia O.; Franco-Duarte, Ricardo; Linhares, João M. M.; et al. "Heterologous expression and structure prediction of a xylanase identified from a compost metagenomic library". Applied Microbiology and Biotechnology 108 1 (2024): http://dx.doi.org/10.1007/s00253-024-13169-4.
    10.1007/s00253-024-13169-4
  5. Duarte-Silva, S; DA SILVA, JORGE D.; Monteiro-Fernandes, Daniela; Costa, Marta Daniela; Neves-Carvalho, Andreia; Raposo, Mafalda; Soares-Cunha, Carina; et al. "Glucocorticoid receptor-dependent therapeutic efficacy of tauroursodeoxycholic acid in preclinical models of Spinocerebellar ataxia type 3 (IF: 19.47)". The Journal of Clinical Investigation (2024):
    Publicado
  6. Duarte-Silva, S; DA SILVA, JORGE D.; Monteiro-Fernandes, Daniela; Costa, Marta Daniela; Neves-Carvalho, Andreia; Raposo, Mafalda; Soares-Cunha, Carina; et al. "Glucocorticoid receptor-dependent therapeutic efficacy of tauroursodeoxycholic acid in preclinical models of Spinocerebellar ataxia type 3". The Journal of Clinical Investigation (2024):
    Publicado
  7. Tatiana F. Vieira; Nuno M. F. S. A. Cerqueira; Manuel Simões; Sérgio F. Sousa. "In silico identification of novel PqsD inhibitors: promising molecules for quorum sensing interference in Pseudomonas aeruginosa". Molecular Systems Design & Engineering (2024): https://doi.org/10.1039/D3ME00107E.
    10.1039/D3ME00107E
  8. Teixeira, Carla S. S.; Biltes, Rita; Villa, Caterina; Sousa, Sérgio F.; Costa, Joana; Ferreira, Isabel M. P. L. V. O.; Mafra, Isabel. "Exploiting Locusta migratoria as a source of bioactive peptides with anti-fibrosis properties using an in silico approach". Food & Function 15 2 (2024): 493-502. http://dx.doi.org/10.1039/d3fo04246d.
    10.1039/d3fo04246d
  9. Fábio G. Martins; Chanchal Kiran Thakur; Chandrabose Karthikeyan; N.S. Hari Narayana Moorthy; Sérgio F. Sousa. "Use of lysinated multiwalled carbon nanotubes with carbohydrate ligands as a doxorubicin nanocarrier: A molecular dynamics analysis". Carbon Trends (2023): https://doi.org/10.1016/j.cartre.2023.100280.
    10.1016/j.cartre.2023.100280
  10. Teixeira, Carla S.S.; Villa, Caterina; Sousa, Sérgio F.; Costa, J; Ferreira, Isabel M.P.L.V.O.; Mafra, Isabel. "An in silico approach to unveil peptides from Acheta domesticus with potential bioactivity against hypertension, diabetes, cardiac and pulmonary fibrosis". Food Research International 169 (2023): 112847. https://doi.org/10.1016/j.foodres.2023.112847.
    Publicado • 10.1016/j.foodres.2023.112847
  11. E. Mauro; D. Lapaillerie; C. Tumiotto; C. Charlier; F. Martins; S. F. Sousa; M. Métifiot; et al. "Modulation of the functional interfaces between retroviral intasomes and the human nucleosome". mBio (2023): https://doi.org/10.1128/mbio.01083-23.
    10.1128/mbio.01083-23
  12. Jovana B. Araškov; Natalia Maciejewska; Mateusz Olszewski; Aleksandar Višnjevac; Vladimir Blagojevic; Henrique S. Fernandes; Sérgio F. Sousa; et al. "Structural, physicochemical and anticancer study of Zn complexes with pyridyl-based thiazolyl-hydrazones". Journal of Molecular Structure (2023): https://doi.org/10.1016/j.molstruc.2023.135157.
    10.1016/j.molstruc.2023.135157
  13. João Carneiro; Rita P. Magalhães; Victor M. de la Oliva Roque; Manuel Simões; Diogo Pratas; Sérgio F. Sousa. "TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa". Journal of Computer-Aided Molecular Design (2023): https://doi.org/10.1007/s10822-023-00505-5.
    10.1007/s10822-023-00505-5
  14. Caroline R. C. Costa; Mariana N. Belchor; Airam Roggero; Laila L. Moraes; Ricardo Samelo; Isabelly Annunciato; Camila R. Bonturi; et al. "The First Anti-Snakebite and Hepatoprotective Characterization of a Trypsin Kunitz-like Inhibitor (EcTI) from the Plant Enterolobium contortisiliquum; A Case of Two Soul Mates Meeting". Pharmaceuticals (2023): https://doi.org/10.3390/ph16040632.
    10.3390/ph16040632
  15. Maria F. Araújo; Elisabete M. S. Castanheira; Sérgio F. Sousa. "The Buzz on Insecticides: A Review of Uses, Molecular Structures, Targets, Adverse Effects, and Alternatives". Molecules (2023): https://doi.org/10.3390/molecules28083641.
    10.3390/molecules28083641
  16. Mariana Novo Belchor; Caroline Ramos da Cruz Costa; Airam Roggero; Laila L. F. Moraes; Ricardo Samelo; Isabelly Annunciato; Marcos Antonio de Oliveira; Sergio F. Sousa; Marcos Hikari Toyama. "In Silico Evaluation of Quercetin Methylated Derivatives on the Interaction with Secretory Phospholipases A2 from Crotalus durissus terrificus and Bothrops jararacussu". Pharmaceuticals (2023): https://doi.org/10.3390/ph16040597.
    10.3390/ph16040597
  17. Sérgio F. Sousa. "Special Issue on “Enzymes as Biocatalysts: Current Research Trends and Applications”". International Journal of Molecular Sciences (2022): https://doi.org/10.3390/ijms232416209.
    10.3390/ijms232416209
  18. Maria José G. Fernandes; Renato B. Pereira; Ana Rita O. Rodrigues; Tatiana F. Vieira; A. Gil Fortes; David M. Pereira; Sérgio F. Sousa; M. Sameiro T. Gonçalves; Elisabete M. S. Castanheira. "Liposomal Formulations Loaded with a Eugenol Derivative for Application as Insecticides: Encapsulation Studies and In Silico Identification of Protein Targets". Nanomaterials (2022): https://doi.org/10.3390/nano12203583.
    10.3390/nano12203583
  19. Henrique S. Fernandes; Nuno M. F. S. A. Cerqueira; Sérgio F. Sousa; André Melo. "A Molecular Mechanics Energy Partitioning Software for Biomolecular Systems". Molecules (2022): https://doi.org/10.3390/molecules27175524.
    10.3390/molecules27175524
  20. Sanja B. Markovic; Natalia Maciejewska; Mateusz Olszewski; Aleksandar Višnjevac; Adrián Puerta; José M. Padrón; Irena Novakovic; et al. "Study of the anticancer potential of Cd complexes of selenazoyl-hydrazones and their sulfur isosters". European Journal of Medicinal Chemistry (2022): https://doi.org/10.1016/j.ejmech.2022.114449.
    10.1016/j.ejmech.2022.114449
  21. Lapaillerie, Delphine ; Charlier, Cathy ; Guyonnet-Dupérat, Véronique ; Murigneux, Emilie; Fernandes, Henrique; Martins, Fábio G.; Magalhães, Rita P.; et al. "Selection of Bis-Indolyl Pyridines and Triphenylamines as New Inhibitors of SARS-CoV-2 Cellular Entry by Modulating the Spike Protein/ACE2 Interfaces.". Antimicrobial agents and chemotherapy (2022): https://europepmc.org/articles/PMC9380551.
    10.1128/aac.00083-22
  22. Juliana F. Rocha; Sérgio F. Sousa; Nuno M. F. Sousa A. Cerqueira. "Computational Studies Devoted to the Catalytic Mechanism of Threonine Aldolase, a Critical Enzyme in the Pharmaceutical Industry to Synthesize ß-Hydroxy-a-amino Acids". ACS Catalysis (2022): 4990-4999. https://doi.org/10.1021/acscatal.1c05567.
    10.1021/acscatal.1c05567
  23. Sara Silva; Joana Marto; Lídia M. Gonçalves; Henrique S. Fernandes; Sérgio F. Sousa; António J. Almeida; Nuno Vale. "Development of Neuropeptide Y and Cell-Penetrating Peptide MAP Adsorbed onto Lipid Nanoparticle Surface". Molecules (2022): https://doi.org/10.3390/molecules27092734.
    10.3390/molecules27092734
  24. Anthony J. Burke; Carla S. S. Teixeira; Sergio F. Sousa. "Front Cover: Transformation of a Chiral Glycolic Acid to an Isoaurone: Stereochemical Assignment of a Benzilic Acid Rearrangment Product (Asian J. Org. Chem. 4/2022)". Asian Journal of Organic Chemistry 11 4 (2022): https://doi.org/10.1002/ajoc.202200050.
    10.1002/ajoc.202200050
  25. Tatiana F. Vieira; Rita P. Magalhães; Manuel Simões; Sérgio F. Sousa. "Drug Repurposing Targeting Pseudomonas aeruginosa MvfR Using Docking, Virtual Screening, Molecular Dynamics, and Free-Energy Calculations". Antibiotics 11 2 (2022): 185-185. https://doi.org/10.3390/antibiotics11020185.
    10.3390/antibiotics11020185
  26. Anthony J. Burke; Carla S. S. Teixeira; Sergio F. Sousa. "Transformation of a Chiral Glycolic Acid to an Isoaurone: Stereochemical Assignment of a Benzilic Acid Rearrangment Product". Asian Journal of Organic Chemistry (2022): https://doi.org/10.1002/ajoc.202100692.
    10.1002/ajoc.202100692
  27. Susana Fernandes; Inês B. Gomes; Sérgio F. Sousa; Manuel Simões. "Antimicrobial Susceptibility of Persister Biofilm Cells of Bacillus cereus and Pseudomonas fluorescens". Microorganisms (2022): https://doi.org/10.3390/microorganisms10010160.
    10.3390/microorganisms10010160
  28. Tatiana F. Vieira; Rita P. Magalhães; Nuno M. F. S. A. Cerqueira; Manuel Simões; Sérgio F. Sousa. "Targeting Pseudomonas aeruginosa MvfR in the battle against biofilm formation: a multi-level computational approach". Molecular Systems Design & Engineering (2022): https://doi.org/10.1039/D2ME00088A.
    10.1039/D2ME00088A
  29. Catarina M. M. Coelho; Renato B. Pereira; Tatiana F. Vieira; Cláudia M. Teixeira; Maria José G. Fernandes; Ana Rita O. Rodrigues; David M. Pereira; et al. "Synthesis, computational and nanoencapsulation studies on eugenol-derived insecticides". New Journal of Chemistry (2022): https://doi.org/10.1039/D2NJ01893D.
    10.1039/D2NJ01893D
  30. Jovana B. Araškov; Aleksandar Višnjevac; Jasminka Popovic; Vladimir Blagojevic; Henrique S. Fernandes; Sérgio F. Sousa; Irena Novakovic; et al. "Zn(ii) complexes with thiazolyl–hydrazones: structure, intermolecular interactions, photophysical properties, computational study and anticancer activity". CrystEngComm (2022): https://doi.org/10.1039/D2CE00443G.
    10.1039/D2CE00443G
  31. Rita P. Magalhães; Henrique S. Fernandes; Sérgio F. Sousa. "The critical role of Asp206 stabilizing residues on the catalytic mechanism of the Ideonella sakaiensis PETase". Catalysis Science & Technology (2022): https://doi.org/10.1039/D1CY02271G.
    10.1039/D1CY02271G
  32. Rita P. Magalhães; Tatiana F. Vieira; André Melo; Sérgio F. Sousa. "Identification of novel candidates for inhibition of LasR, a quorum-sensing receptor of multidrug resistant Pseudomonas aeruginosa, through a specialized multi-level in silico approach". Molecular Systems Design & Engineering (2022): https://doi.org/10.1039/D2ME00009A.
    10.1039/D2ME00009A
  33. Ana Cláudia Pereira; André F. Pina; Diana Sousa; Débora Ferreira; Cátia Santos-Pereira; Joana L. Rodrigues; Luís D. R. Melo; et al. "Identification of novel aptamers targeting cathepsin B-overexpressing prostate cancer cells". Molecular Systems Design & Engineering (2022): https://doi.org/10.1039/D2ME00022A.
    10.1039/D2ME00022A
  34. Carla S. S. Teixeira; Sérgio F. Sousa. "Current Status of the Use of Multifunctional Enzymes as Anti-Cancer Drug Targets". Pharmaceutics (2021): https://doi.org/10.3390/pharmaceutics14010010.
    10.3390/pharmaceutics14010010
  35. "Identification of Tripeptides against Tyrosine Kinase Domain of EGFR for Lung Cancer Cell Inhibition by In silico and In vitro Studies". Chemical Biology & Drug Design (2021): http://dx.doi.org/10.1111/cbdd.14010.
    10.1111/cbdd.14010
  36. André F. Pina; Sérgio F. Sousa; Nuno M. F. S. A. Cerqueira. "The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys-His-Glu Triad: A Computational Study". ChemBioChem (2021): https://doi.org/10.1002/cbic.202100555.
    10.1002/cbic.202100555
  37. "Assessing the effects of PMM2 variants on protein stability". Molecular Genetics and Metabolism 134 4 (2021): 344-352. http://dx.doi.org/10.1016/j.ymgme.2021.11.002.
    10.1016/j.ymgme.2021.11.002
  38. Rita P. Magalhães; Jorge M. Cunha; Sérgio F. Sousa. "Perspectives on the Role of Enzymatic Biocatalysis for the Degradation of Plastic PET". International Journal of Molecular Sciences 22 20 (2021): 11257-11257. https://doi.org/10.3390/ijms222011257.
    10.3390/ijms222011257
  39. José P. Leite; Marta G. Lete; Susan B. Fowler; Ana Gimeno; Juliana F. Rocha; Sérgio F. Sousa; Carl I. Webster; Jesús J. Jiménez-Bar`bero; Luís Gales. "Aß31–35 Decreases Neprilysin-Mediated Alzheimer’s Amyloid-ß Peptide Degradation". ACS Chemical Neuroscience (2021): https://doi.org/10.1021/acschemneuro.1c00432.
    10.1021/acschemneuro.1c00432
  40. Tatiana F. Vieira; Fábio Martins; Joel P. Moreira; Tiago Barbosa; Sergio F. Sousa. "In Silico Identification of Possible Inhibitors for Protein Kinase B (PknB) of Mycobacterium tuberculosis". Molecules (2021): https://www.mdpi.com/1420-3049/26/20/6162.
    10.3390/molecules26206162
  41. Henrique S. Fernandes; Sérgio F. Sousa; Nuno M. F. S. A. Cerqueira. "New insights into the catalytic mechanism of the SARS-CoV-2 main protease: an ONIOM QM/MM approach". Molecular Diversity (2021): https://doi.org/10.1007/s11030-021-10259-7.
    10.1007/s11030-021-10259-7
  42. Paula Mihaljevic-Juric; Sérgio F. Sousa. "A QM/MM Evaluation of the Missing Step in the Reduction Mechanism of HMG-CoA by Human HMG-CoA Reductase". Processes (2021): https://doi.org/10.3390/pr9071085.
    10.3390/pr9071085
  43. Henrique S. Fernandes; Nuno M. F. S. A. Cerqueira; Sérgio F. Sousa. "Developing and Using BioSIMAR, an Augmented Reality Program to Visualize and Learn about Chemical Structures in a Virtual Environment on Any Internet-Connected Device". Journal of Chemical Education 98 5 (2021): 1789-1794. https://doi.org/10.1021/acs.jchemed.0c01317.
    10.1021/acs.jchemed.0c01317
  44. Fábio Martins; André Melo; Sergio F. Sousa. "Identification of New Potential Inhibitors of Quorum Sensing through a Specialized Multi-Level Computational Approach". Molecules (2021): https://www.mdpi.com/1420-3049/26/9/2600.
    10.3390/molecules26092600
  45. Delphine Lapaillerie; Cathy Charlier; Henrique S. Fernandes; Sergio F. Sousa; Paul Lesbats; Pierre Weigel; Alexandre Favereaux; Véronique Guyonnet-Duperat; Vincent Parissi. "In Silico, In Vitro and In Cellulo Models for Monitoring SARS-CoV-2 Spike/Human ACE2 Complex, Viral Entry and Cell Fusion". Viruses (2021): https://doi.org/10.3390/v13030365.
    10.3390/v13030365
  46. Fábio G. Martins; André Melo; Sérgio F. Sousa. "Databases for the study of biofilms: current status and potential applications". Biofouling (2021): https://doi.org/10.1080/08927014.2021.1876849.
    10.1080/08927014.2021.1876849
  47. Sérgio F. Sousa. "Special Issue on “The Application of Quantum Mechanics in Reactivity of Molecules”". Applied Sciences 11 3 (2021): 1132-1132. https://doi.org/10.3390/app11031132.
    10.3390/app11031132
  48. Ribeiro, P.M.G.; Fernandes, H.S.; Maia, L.B.; Sousa, S.F.; Moura, J.J.G.; Cerqueira, N.M.F.S.A.; Pedro M. G. Ribeiro; et al. "The complete catalytic mechanism of xanthine oxidase: A computational study". Inorganic Chemistry Frontiers 8 2 (2021): 405-416. http://www.scopus.com/inward/record.url?eid=2-s2.0-85100037271&partnerID=MN8TOARS.
    10.1039/d0qi01029d
  49. Gonçalves, I.G.; Fernandes, H.S.; Melo, A.; Sousa, S.F.; Simões, L.C.; Simões, M.. "LegionellaDB – A Database on Legionella Outbreaks". Trends in Microbiology (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85101362901&partnerID=MN8TOARS.
    10.1016/j.tim.2021.01.015
  50. Brás, N.F.; Neves, R.P.P.; Lopes, F.A.A.; Correia, M.A.S.; Palma, A.S.; Sousa, S.F.; Ramos, M.J.. "Combined in silico and in vitro studies to identify novel antidiabetic flavonoids targeting glycogen phosphorylase". Bioorganic Chemistry 108 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85098077714&partnerID=MN8TOARS.
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  51. Silva Teixeira, C.S.; Sousa, S.F.; Cerqueira, N.M.F.S.A.. "An Unsual Cys-Glu-Lys Catalytic Triad is Responsible for the Catalytic Mechanism of the Nitrilase Superfamily: A QM/MM Study on Nit2". ChemPhysChem (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85103011747&partnerID=MN8TOARS.
    10.1002/cphc.202000751
  52. Carolina M. Natal; Maria José G. Fernandes; Nuno F. S. Pinto; Renato B. Pereira; Tatiana F. Vieira; Ana Rita O. Rodrigues; David M. Pereira; et al. "New carvacrol and thymol derivatives as potential insecticides: synthesis, biological activity, computational studies and nanoencapsulation". RSC Advances (2021): https://doi.org/10.1039/D1RA05616F.
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  53. Santos-Pereira, C.; Rocha, J.F.; Fernandes, H.S.; Rodrigues, L.R.; Côrte-Real, M.; Sousa, S.F.. "The milk-derived lactoferrin inhibits V-ATPase activity by targeting its V1 domain". International Journal of Biological Macromolecules 186 (2021): 54-70. http://www.scopus.com/inward/record.url?eid=2-s2.0-85109463515&partnerID=MN8TOARS.
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  54. Serrano, C.; Teixeira, C.S.S.; Cooper, D.N.; Carneiro, J.; Lopes-Marques, M.; Stenson, P.D.; Amorim, A.; et al. "Compensatory epistasis explored by molecular dynamics simulations". Human Genetics 140 9 (2021): 1329-1342. http://www.scopus.com/inward/record.url?eid=2-s2.0-85108789594&partnerID=MN8TOARS.
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  55. Pereira, R.B.; Pinto, N.F.S.; Fernandes, M.J.G.; Vieira, T.F.; Rodrigues, A.R.O.; Pereira, D.M.; Sousa, S.F.; et al. "Amino alcohols from eugenol as potential semisynthetic insecticides: Chemical, biological, and computational insights". Molecules 26 21 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85118383420&partnerID=MN8TOARS.
    10.3390/molecules26216616
  56. Carla Sílvia Silva Teixeira; Nuno M. F. S. A. Cerqueira; Sérgio Filipe Sousa. "Multifunctional Enzymes as Targets for the Treatment of Tuberculosis: Paving the Way for New Anti-TB Drugs". Current Medicinal Chemistry (2020): https://doi.org/10.2174/0929867328666201229122722.
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  57. Ana Cláudia Pereira; Débora Ferreira; Cátia Santos-Pereira; Tatiana F. Vieira; Sérgio F. Sousa; Goreti Sales; Lígia R. Rodrigues. "Selection of a new peptide homing SK-BR-3 breast cancer cells". Chemical Biology & Drug Design (2020): https://doi.org/10.1111/cbdd.13816.
    10.1111/cbdd.13816
  58. Carla S. S. Teixeira; Nuno M. F. S. A. Cerqueira; Pedro Gomes; Sérgio F. Sousa. "A Molecular Perspective on Sirtuin Activity". International Journal of Molecular Sciences (2020): https://doi.org/10.3390/ijms21228609.
    10.3390/ijms21228609
  59. Tatiana F. Vieira; Maria F. Araújo; Maria José G. Fernandes; David M. Pereira; A. Gil Fortes; Elisabete M. S. Castanheira; M. Sameiro T. Gonçalves; Sérgio F. Sousa. "In Silico Identification of Protein Targets Associated to the Insecticide Activity of Eugenol Derivatives". Chemistry Proceedings 3 1 (2020): 138-138. https://doi.org/10.3390/ecsoc-24-08333.
    10.3390/ecsoc-24-08333
  60. Diana S. Gesto; Carlos M. S. Pereira; Nuno M. F. S. Cerqueira; Sérgio F. Sousa. "An Atomic-Level Perspective of HMG-CoA-Reductase: The Target Enzyme to Treat Hypercholesterolemia". Molecules (2020): https://doi.org/10.3390/molecules25173891.
    10.3390/molecules25173891
  61. Sérgio F. Sousa; Ana R. Calixto; Pedro Ferreira; Maria J. Ramos; Carmay Lim; Pedro A. Fernandes. "Activation Free Energy, Substrate Binding Free Energy, and Enzyme Efficiency Fall in a Very Narrow Range of Values for Most Enzymes". ACS Catalysis (2020): 8444-8453. https://doi.org/10.1021/acscatal.0c01947.
    10.1021/acscatal.0c01947
  62. Rita P. Magalhães; Henriques S. Fernandes; Sérgio F. Sousa; Magalhães, Rita P.; Fernandes, Henrique S.; Sousa, Sérgio F.. "Modelling Enzymatic Mechanisms with QM/MM Approaches: Current Status and Future Challenges". Israel Journal of Chemistry 60 7 (2020): 655-666. https://doi.org/10.1002/ijch.202000014.
    No prelo • 10.1002/ijch.202000014
  63. Sousa, Sérgio F.. "Reaction Mechanism and Determinants for Efficient Catalysis by DszB, a Key Enzyme for Crude Oil Biodesulfurization". ACS Catalysis (2020): http://dx.doi.org/10.1021/acscatal.0c03122.
    10.1021/acscatal.0c03122
  64. Magalhães, Rita P.; Vieira, Cláudia Tatiana Freitas; Simões, Manuel; Melo, André S.; Fernandes, Henrique S.; Sousa, Sérgio F.. "The Biofilms Structural Database". Trends in Biotechnology (IF 13.75) (10.1016/j.tibtech.2020.04.002) (in press) (2020):
    No prelo • 10.1016/j.tibtech.2020.04.002
  65. Sousa, S.F.; Simões, M.; Filipovic, N.. "Editorial: The Chemistry of Biofilms and Their Inhibitors". Frontiers in Chemistry 8 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85090269067&partnerID=MN8TOARS.
    10.3389/fchem.2020.00746
  66. Henrique S. Fernandes; Sérgio F. Sousa; Nuno M. F. S. A. Cerqueira. "VMD Store–A VMD Plugin to Browse, Discover, and Install VMD Extensions". Journal of Chemical Information and Modeling (2019): https://doi.org/10.1021/acs.jcim.9b00739.
    10.1021/acs.jcim.9b00739
  67. Tatiana F. Vieira; Sérgio F. Sousa. "Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual Screening". Applied Sciences (2019): https://doi.org/10.3390/app9214538.
    10.3390/app9214538
  68. Carla S. Silva Teixeira; Maria J. Ramos; Sérgio F. Sousa; Nuno M. F. S. A. Cerqueira. "Solving the Catalytic Mechanism of Tryptophan Synthase: an Emergent Drug Target in the Treatment of Tuberculosis". ChemCatChem (2019): https://doi.org/10.1002/cctc.201901505.
    10.1002/cctc.201901505
  69. Henrique S. Fernandes; Carla S. Silva Teixeira; Sérgio F. Sousa; Nuno M. F. S. A. Cerqueira. "Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview". Molecules 24 13 (2019): 2462-2462. https://doi.org/10.3390/molecules24132462.
    10.3390/molecules24132462
  70. Sousa, Sérgio F.. "Human Fatty Acid Synthase: A Computational Study of the Transfer of the Acyl Moieties from MAT to the ACP Domain". ChemCatChem (2019): http://dx.doi.org/10.1002/cctc.201900548.
    10.1002/cctc.201900548
  71. Sousa, Sérgio F.. "Tailoring Specialized Scoring Functions For More Efficient Virtual Screening". Frontiers in Drug, Chemistry and Clinical Research (2019):
    10.15761/FDCCR.1000118
  72. Juliana F. Rocha; André F. Pina; Sérgio F. Sousa; Nuno M. F. S. A. Cerqueira; Rocha, J.F.; Pina, A.F.; Sousa, S.F.; Cerqueira, N.M.F.S.A.. "PLP-dependent enzymes as important biocatalysts for the pharmaceutical, chemical and food industries: a structural and mechanistic perspective". Catalysis Science & Technology 9 18 (2019): 4864-4876. https://doi.org/10.1039/C9CY01210A.
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  73. Sousa, Sergio F.; Neves, Rui P. P.; Waheed, Sodiq O.; Fernandes, Pedro A.; Ramos, Maria Joao; Sousa, Sérgio F.. "Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins". Biological Chemistry (2019): https://publons.com/publon/18724975/.
    10.1515/HSZ-2018-0319
  74. Soares, S.; García-Estévez, I.; Ferrer-Galego, R.; Brás, N.F.; Brandão, E.; Silva, M.; Teixeira, N.; et al. "Study of human salivary proline-rich proteins interaction with food tannins". Food Chemistry 243 (2018): 175-185. http://www.scopus.com/inward/record.url?eid=2-s2.0-85030457914&partnerID=MN8TOARS.
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  75. Biernacki, K.; Sousa, S.F.; Gales, L.; Ramos, M.J.; Magalhães, A.L.; Krzysztof Biernacki; Sergio F. Sousa; et al. "Transport Properties of Light Gases in Nanochannels of L–Leu-L-Ser Dipeptide Crystals: A Comparative Study by Molecular Dynamics Simulations". ChemistrySelect 3 20 (2018): 5517-5525. http://www.scopus.com/inward/record.url?eid=2-s2.0-85047658538&partnerID=MN8TOARS.
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  76. Barbosa, A.C.C.; Neves, R.P.P.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.; Ana C. C. Barbosa; Rui P. P. Neves; et al. "Mechanistic Studies of a Flavin Monooxygenase: Sulfur Oxidation of Dibenzothiophenes by DszC". ACS Catalysis (2018): 9298-9311. http://www.scopus.com/inward/record.url?eid=2-s2.0-85053179304&partnerID=MN8TOARS.
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  77. Pedro Paiva; Sérgio F. Sousa; Maria J. Ramos; Pedro A. Fernandes; Sousa, Sérgio. "Understanding the Catalytic Machinery and the Reaction Pathway of the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase". ACS Catalysis 0 0 (2018): 4860-4872. https://publons.com/publon/8944609/.
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  78. Sergio F. Sousa; Joana Peres; Manuel Coelho; Tatiana F. Vieira; Sousa, S.F.; Peres, J.; Coelho, M.; Vieira, T.F.. "Analyzing PEGylation through Molecular Dynamics Simulations". ChemistrySelect 3 29 (2018): 8415-8427. https://publons.com/publon/14216409/.
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  79. Sousa, S.F.; Ribeiro, A.J.M.; Neves, R.P.P.; Brás, N.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.; et al. "Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms". Wiley Interdisciplinary Reviews: Computational Molecular Science 7 2 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-84984706224&partnerID=MN8TOARS.
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  80. Ferreira, P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.; Ferreira, Pedro; Sousa, Sergio F.; Fernandes, Pedro A.; Ramos, Maria Joao. "Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives". Chemistry - A European Journal 23 68 (2017): 17231-17241. http://www.scopus.com/inward/record.url?eid=2-s2.0-85034791783&partnerID=MN8TOARS.
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  81. Oliveira, E.F.; Santos-Martins, D.; Ribeiro, A.M.; Brás, N.F.; Cerqueira, N.S.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015)". Expert Opinion on Therapeutic Patents 26 11 (2016): 1257-1272. http://www.scopus.com/inward/record.url?eid=2-s2.0-84992043959&partnerID=MN8TOARS.
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  82. Moorthy, N.S.H.N.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery". Journal of Enzyme Inhibition and Medicinal Chemistry 31 6 (2016): 1428-1442. http://www.scopus.com/inward/record.url?eid=2-s2.0-84958778405&partnerID=MN8TOARS.
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  86. Cerqueira, Nuno M. F. S. A.; Gesto, Diana; Oliveira, Eduardo F.; Santos-Martins, Diogo; Bras, Natercia F.; Sousa, Sergio F.; Fernandes, Pedro A.; Ramos, Maria J.. "Receptor-based virtual screening protocol for drug discovery". Archives of Biochemistry and Biophysics 582 (2015): 56-67. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000360781200007&KeyUID=WOS:000360781200007.
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  90. Moorthy, N. S. Hari Narayana; Martins, Silvia A.; Sousa, Sergio F.; Ramos, Maria J.; Fernandes, Pedro A.. "Classification study of solvation free energies of organic molecules using machine learning techniques". Rsc Advances 4 106 (2014): 61624-61630. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000345656600051&KeyUID=WOS:000345656600051.
    10.1039/c4ra07961b
  91. Marcial, B.L.; Sousa, S.F.; Santos, H.F.D.; Ramos, M.J.. "Structural and dynamics analysis of matrix metalloproteinases MMP-2 complexed with chemically modified tetracyclines (CMTs)". Journal of Biomolecular Structure and Dynamics 32 12 (2014): 1907-1918. http://www.scopus.com/inward/record.url?eid=2-s2.0-84906302907&partnerID=MN8TOARS.
    10.1080/07391102.2013.842186
  92. 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
  93. Sergio Sousa; Nuno M. F. S. A. Cerqueira; Natércia F. Brás; Pedro A. Fernandes; Maria J. Ramos. "Enzymatic "Tricks": Carboxylate Shift and Sulfur Shift". International Journal of Quantum Chemistry (2014): https://publons.com/publon/1616008/.
    10.1002/QUA.24689
  94. Sérgio Filipe Sousa. "DNA (Química Biológica)". Revista de Ciência Elementar 1 1 (2013): https://doi.org/10.24927/rce2013.050.
    10.24927/rce2013.050
  95. 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
  96. Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Parameters for molecular dynamics simulations of manganese-containing metalloproteins". Journal of Chemical Theory and Computation 9 6 (2013): 2718-2732. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879120460&partnerID=MN8TOARS.
    10.1021/ct400055v
  97. Moorthy, N.S.H.N.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "Farnesyltransferase inhibitors: A comprehensive review based on quantitative structural analysis". Current Medicinal Chemistry 20 38 (2013): 4888-4923. http://www.scopus.com/inward/record.url?eid=2-s2.0-84889569673&partnerID=MN8TOARS.
    10.2174/09298673113206660262
  98. Sílvia A. Martins; Marta A. S. Perez; Irina S. Moreira; Sergio Sousa; M. J. Ramos; P. A. Fernandes; Martins, S.A.; et al. "Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI". Journal of Chemical Theory and Computation 9 3 (2013): 1311-1319. https://publons.com/publon/1616011/.
    10.1021/CT4000372
  99. Silvia A. Martins; Sergio Sousa; Martins, S.A.; Sousa, S.F.. "Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules". Journal of Computational Chemistry 34 15 (2013): 1354-1362. https://publons.com/publon/1616010/.
    10.1002/JCC.23264
  100. Sousa, Sergio F.; Coimbra, Joao T. S.; Paramos, Diogo; Pinto, Rita; Guimares, Rodrigo S.; Teixeira, Vitor; Fernandes, Pedro A.; et al. "Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif". Journal of Molecular Modeling 19 2 (2013): 673-688. https://publons.com/publon/1616012/.
    10.1007/S00894-012-1590-1
  101. 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
  102. Valente, M.; Sousa, S.F.; Magalhães, A.L.; Freire, C.; Valente, Mario; Sousa, Sergio Filipe; Magalhaes, Alexandre L.; Freire, Cristina. "Dehydration of a polyether type extraction agent and of the corresponding K+ complex: Insights into liquid-liquid extraction mechanisms by quantum chemical methods". Journal of Molecular Modeling 18 11 (2012): 4909-4915. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870546403&partnerID=MN8TOARS.
    10.1007/s00894-012-1491-3
  103. Moorthy, N.S.H.N.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "In silico based structural analysis of some piperidine analogs as farnesyltransferase inhibitors". Medicinal Chemistry 8 5 (2012): 853-864. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865803335&partnerID=MN8TOARS.
    10.2174/157340612802084171
  104. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.; Sergio Sousa; Pedro Alexandrino Fernandes; Maria João Ramos. "Computational enzymatic catalysis - Clarifying enzymatic mechanisms with the help of computers". Physical Chemistry Chemical Physics 14 36 (2012): 12431-12441. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865477079&partnerID=MN8TOARS.
    10.1039/c2cp41180f
  105. Valente, Mario; Sousa, Sergio Filipe; Magalhaes, A. L.; Freire, Cristina; Valente, M.; Sousa, S.F.; Magalhães, A.L.; Freire, C.. "Decomplexation and complexation of alkali metal cations by a crown-ether-type podand in dichloromethane: a steered molecular dynamics study". Theoretica Chimica Acta 131 3 (2012): 1-7. https://publons.com/publon/1616017/.
    10.1007/S00214-012-1171-5
  106. Mário Valente; Sergio Sousa; A. L. Magalhães; Cristina Freire. "Transfer of the K + Cation Across a Water/Dichloromethane Interface: A Steered Molecular Dynamics Study with Implications in Cation Extraction". The Journal of Physical Chemistry B (2012): https://publons.com/publon/1616021/.
    10.1021/JP210786J
  107. Bruna L. Marcial; Sergio Sousa; Ingrid L. Barbosa; Helio F. Dos Santos; Maria J. Ramos; Marcial, B.L.; Sousa, S.F.; et al. "Chemically Modified Tetracyclines as Inhibitors of MMP-2 Matrix Metalloproteinase: A Molecular and Structural Study". The Journal of Physical Chemistry B 116 46 (2012): 13644-13654. https://publons.com/publon/1616015/.
    10.1021/JP3079748
  108. Valente, M.; Sousa, S.F.; Magalhaes, A.L.; Freire, C.; Valente, Mario; Sousa, Sergio Filipe; Magalhaes, Alexandre L.; Freire, Cristina. "Complexation of alkali metal cations by crown-ether type podands with applications in solvent extraction: Insights from quantum chemical calculations". Journal of Molecular Modeling 17 12 (2011): 3275-3288. http://www.scopus.com/inward/record.url?eid=2-s2.0-84855676892&partnerID=MN8TOARS.
    10.1007/s00894-011-1004-9
  109. Narayana Moorthy, N.S.H.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "In silico-based structural analysis of arylthiophene derivatives for FTase inhibitory activity, hERG, and other toxic effects". Journal of Biomolecular Screening 16 9 (2011): 1037-1046. http://www.scopus.com/inward/record.url?eid=2-s2.0-80053498208&partnerID=MN8TOARS.
    10.1177/1087057111414899
  110. Hari Narayana Moorthy, N.S.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors". Journal of Enzyme Inhibition and Medicinal Chemistry 26 6 (2011): 777-791. http://www.scopus.com/inward/record.url?eid=2-s2.0-81355138323&partnerID=MN8TOARS.
    10.3109/14756366.2011.552885
  111. Marta A. S. Perez; Sergio Sousa; Eduardo F. T. Oliveira; Pedro A. Fernandes; Maria J. Ramos. "Detection of Farnesyltransferase Interface Hot Spots through Computational Alanine Scanning Mutagenesis". The Journal of Physical Chemistry B (2011): https://publons.com/publon/1616024/.
    10.1021/JP205481Y
  112. Sergio Sousa; Bruno Tamames; Pedro Alexandrino Fernandes; Maria Joa~o Ramos. "Detailed Atomistic Analysis of the HIV-1 Protease Interface". The Journal of Physical Chemistry B (2011): https://publons.com/publon/1616023/.
    10.1021/JP200075S
  113. Sergio F. Sousa. "COMPUTATIONAL PROTEOMICS - FROM METHODOLOGICAL DEVELOPMENTS TO BIOLOGICAL APPLICATIONS". Quantal Aspects in Chemistry and Physics: a Tribute to the Memory of Professor Couceiro da Costa (2011): https://publons.com/publon/14216410/.
  114. Valente, M.; Sousa, S.F.; Magalhães, A.L.; Freire, C.; Valente, Mario; Sousa, Sergio Filipe; Magalhaes, A. L.; Freire, Cristina. "Factors influencing the binding of a potassium cation to a polyethylene glycol type podand in liquid-liquid extraction-a molecular dynamics study". Theoretical Chemistry Accounts 127 5 (2010): 681-687. http://www.scopus.com/inward/record.url?eid=2-s2.0-78149429191&partnerID=MN8TOARS.
    10.1007/s00214-010-0778-7
  115. Sousa, S.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Virtual screening in drug design and development". Combinatorial Chemistry and High Throughput Screening 13 5 (2010): 442-453. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955767207&partnerID=MN8TOARS.
    10.2174/138620710791293001
  116. Valente, Mario; Sousa, Sergio Filipe; Magalhaes, Alexandre Lopes; Freire, Cristina. "Crown-Ether Type Podands as Alkali Metal Cation Extractants: Influence of the Number of Oxygens in the Chain". Journal of Solution Chemistry (2010): https://publons.com/publon/1616028/.
    10.1007/S10953-010-9579-9
  117. Mário Valente; Sergio Sousa; A.L. Magalhães; Cristina Freire; Valente, M.; Sousa, S.F.; Magalhães, A.L.; Freire, C.. "A comparative molecular dynamics study on the complexation of alkali metal cations by a poly-ethylene-glycol type podand in water and in dichloromethane". Computational and Theoretical Chemistry 946 1-3 (2010): 77-82. https://publons.com/publon/1616026/.
    10.1016/J.THEOCHEM.2009.10.025
  118. Sousa, Sérgio F.. "Recent Advances On Computational Proteomics". Proceedings of the WASET Conference, Singapore (2009): https://zenodo.org/record/1085107.
    10.5281/zenodo.1085107
  119. Sousa, S.F.; Cerqueira, N.M.F.S.A.; Perez, M.A.S.; Moreira, I.S.; Ribeiro, A.J.M.; Neves, A.R.A.P.; Ramos, M.J.; Fernandes, P.A.. "Recent advances on computational proteomics". World Academy of Science, Engineering and Technology 56 (2009): 376-386. http://www.scopus.com/inward/record.url?eid=2-s2.0-78651571830&partnerID=MN8TOARS.
  120. Cerqueira, N.M.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Virtual screening of compound libraries.". Methods in molecular biology (Clifton, N.J.) 572 (2009): 57-70. http://www.scopus.com/inward/record.url?eid=2-s2.0-79952110876&partnerID=MN8TOARS.
  121. Sousa, S.F.; Carvalho, E.S.; Ferreira, D.M.; Tavares, I.S.; Fernandes, P.A.; Ramos, M.J.; Gomes, J.A.N.F.. "Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes". Journal of Computational Chemistry 30 16 (2009): 2752-2763. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349932424&partnerID=MN8TOARS.
    10.1002/jcc.21304
  122. Pande, V.; Sousa, S.F.; Ramos, M.J.. "Direct covalent modification as a strategy to inhibit Nuclear Factor-Kappa B". Current Medicinal Chemistry 16 32 (2009): 4261-4273. http://www.scopus.com/inward/record.url?eid=2-s2.0-70450198853&partnerID=MN8TOARS.
    10.2174/092986709789578222
  123. Sergio Sousa; Pedro Alexandrino Fernandes; Maria João Ramos. "The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase". Chemistry - A European Journal (2009): https://publons.com/publon/1616035/.
    10.1002/CHEM.200802745
  124. Sergio Sousa; Pedro Alexandrino Fernandes; Maria Joa~o Ramos. "Gas-Phase Geometry Optimization of Biological Molecules as a Reasonable Alternative to a Continuum Environment Description: Fact, Myth, or Fiction?". The Journal of Physical Chemistry A (2009): https://publons.com/publon/1616033/.
    10.1021/JP902213T
  125. Sergio Sousa; Ana Branca Lopes; Pedro Alexandrino Fernandes; Maria João Ramos; Sousa, S.F.; Lopes, A.B.; Fernandes, P.A.; Ramos, M.J.. "The Zinc proteome: a tale of stability and functionality". Dalton Transactions 38 (2009): 7946-7956. https://publons.com/publon/1616036/.
    10.1039/B904404C
  126. Sergio Sousa; Pedro Alexandrino Fernandes; Maria João Ramos; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme". Bioorganic & Medicinal Chemistry 17 9 (2009): 3369-3378. https://publons.com/publon/1616034/.
    10.1016/J.BMC.2009.03.055
  127. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Farnesyltransferase inhibitors: A detailed chemical view on an elusive biological problem". Current Medicinal Chemistry 15 15 (2008): 1478-1492. http://www.scopus.com/inward/record.url?eid=2-s2.0-47349089381&partnerID=MN8TOARS.
    10.2174/092986708784638825
  128. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.; Sergio Sousa; Pedro A. Fernandes; Maria Joa~o Ramos. "Enzyme flexibility and the catalytic mechanism of farnesyltransferase: Targeting the relation". Journal of Physical Chemistry B 112 29 (2008): 8681-8691. http://www.scopus.com/inward/record.url?eid=2-s2.0-49149110925&partnerID=MN8TOARS.
    10.1021/jp711214j
  129. Sergio Sousa; Pedro A. Fernandes; Maria João Ramos; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics analysis of farnesyltransferase: A closer look into the amino acid behavior". International Journal of Quantum Chemistry 108 11 (2008): 1939-1950. https://publons.com/publon/1616040/.
    10.1002/QUA.21713
  130. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.; Sergio Sousa; Pedro Alexandrino Fernandes; Maria João Ramos. "Theoretical studies on farnesyltransferase: The distances paradox explained". Proteins: Structure, Function and Genetics 66 1 (2007): 205-218. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845671721&partnerID=MN8TOARS.
    10.1002/prot.21219
  131. Sergio Sousa; Pedro Alexandrino Fernandes; Maria João Ramos; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "General performance of density functionals". The Journal of Physical Chemistry A 111 42 (2007): 10439-10452. https://publons.com/publon/1616044/.
    10.1021/JP0734474
  132. Sergio Sousa; Pedro Alexandrino Fernandes; Maria João Ramos; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere". Journal of Computational Chemistry 28 7 (2007): 1160-1168. https://publons.com/publon/1616047/.
    10.1002/JCC.20577
  133. Sergio Sousa; Pedro A. Fernandes; Maria João Ramos; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "The Carboxylate Shift in Zinc Enzymes: A Computational Study". Journal of the American Chemical Society 129 5 (2007): 1378-1385. https://publons.com/publon/1616045/.
    10.1021/JA067103N
  134. Sousa, Sergio Filipe; Fernandes, Pedro Alexandrino; Ramos, Maria Joao; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism". Theoretica Chimica Acta 117 1 (2007): 171-181. https://publons.com/publon/1616043/.
    10.1007/S00214-006-0170-9
  135. Sergio Sousa; Pedro Alexandrino Fernandes; Maria João Ramos. "Comparative Assessment of Theoretical Methods for the Determination of Geometrical Properties in Biological Zinc Complexes". The Journal of Physical Chemistry B (2007): https://publons.com/publon/1616041/.
    10.1021/JP072538Y
  136. Sergio Sousa; Bruno Tamames; Pedro Alexandrino Fernandes; Maria João Ramos; Tamames, B.; Sousa, S.F.; Tamames, J.; Fernandes, P.A.; Ramos, M.J.. "Analysis of zinc-ligand bond lengths in metalloproteins: Trends and patterns". Proteins: Structure, Function, and Bioinformatics 69 3 (2007): 466-475. https://publons.com/publon/1616042/.
    10.1002/PROT.21536
  137. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.; Sergio Sousa; Pedro Alexandrino Fernandes; Maria João Ramos. "Protein-ligand docking: Current status and future challenges". Proteins: Structure, Function and Genetics 65 1 (2006): 15-26. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748276474&partnerID=MN8TOARS.
    10.1002/prot.21082
  138. Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Farnesyltransferase: Theoretical studies on peptide substrate entrance - Thiol or thiolate coordination?". Journal of Molecular Structure: THEOCHEM 729 1-2 SPEC. (2005): 125-129. http://www.scopus.com/inward/record.url?eid=2-s2.0-24344434552&partnerID=MN8TOARS.
    10.1016/j.theochem.2005.03.022
  139. Sousa, SF; Fernandes, PA; Ramos, MJ; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Unraveling the mechanism of the farnesyltransferase enzyme". Journal of Biological Inorganic Chemistry 10 1 (2005): 3-10. https://publons.com/publon/1616052/.
    10.1007/S00775-004-0612-6
  140. Sergio Sousa; Pedro A. Fernandes; Maria João Ramos. "Farnesyltransferase—New Insights into the Zinc-Coordination Sphere Paradigm: Evidence for a Carboxylate-Shift Mechanism". Biophysical Journal (2005): https://publons.com/publon/1616050/.
    10.1529/BIOPHYSJ.104.048207
  141. Fernandes, P.A.; Carvalho, A.T.P.; Marques, A.T.; Pereira, A.L.F.; Madeira, A.P.S.; Ribeiro, A.S.P.; Carvalho, A.F.R.; et al. "New designs for MRI contrast agents". Journal of Computer-Aided Molecular Design 17 7 (2003): 463-473. http://www.scopus.com/inward/record.url?eid=2-s2.0-0344271775&partnerID=MN8TOARS.
    10.1023/A:1027347527385
Capítulo de livro
  1. Sousa, Sérgio F.. "Structural Characterization of Membrane Protein Dimers". 2019.
    10.1007/978-1-4939-9161-7_21
  2. Teixeira, C. S. S.; Fernandes, H. S.; Sousa, Sérgio F.; Cerqueira, N.M.F.S.A.. "Enzymatic Amino Acid Deprivation Therapies Targeting Cancer". In Pharmaceutical Biocatalysis: Fundamentals, Enzyme Inhibitors, and Enzymes in Health and Diseases, editado por Grunwald, P., 311-347. Pan Stanford Publishing Pte. Ltd., 2019.
    Publicado
  3. Sousa, Sergio F.; Coimbra, Joao T. S.; Fernandes, Pedro A.; Marino, Tiziana; Ramos, Maria J.; Russo, Nino; Nascimento, MAC; et al. "Molecular Dynamics Analysis of FAAH Complexed with Anandamide". 114-130. 2015.
    10.1007/978-3-319-14397-2_7
  4. Brás, Natércia .F.; Coimbra, João T. S.; Neves, Rui P. P.; Cerqueira, Nuno M. F. S. A.; Sousa, Sérgio F.; Fernandes, Pedro A.; Ramos, Maria J.. "Computational Biochemistry". In Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. -: Elsevier, 2015.
    10.1016/b978-0-12-409547-2.10833-9
  5. Brás, N.F.; Cerqueira, N.M.F.S.A.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Protein ligand docking in drug discovery". 2014.
    10.1007/978-3-319-09976-7_11
  6. Sousa, Sérgio F.; Martins, S.; Fernandes, P. A.. "A Quimica Computacional e os Medicamentos". In Quimica do Dia-a-Dia, editado por Sotomayor, J.. Gradiva, 2014.
  7. Sousa, Sérgio F.; Fernandes, P.A.; Ramos, M. J.. "Computational Studies on the Mechanism of Farnesyltransferase". In Computational studies of enzyme mechanisms, editado por Mullholand, A.. Springer, 2012.
    Publicado
  8. Sousa, Sérgio F.. "Computational proteomics: from methodological developments to biological applications". 2011.
    10.14195/978-989-26-0240-0_8
  9. Sousa, Sérgio F.. "Virtual Screening of Compound Libraries". 2010.
    10.1007/978-1-60761-244-5_4
  10. Sousa, Sérgio F.. "Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes". 2010.
    10.1007/978-90-481-3034-4_11
  11. Sousa, Sérgio F.; Ramos, M.J. "The Ins and Outs of QM/MM Calculations: Current Status and Future Challenges". In Computational Proteomics, editado por Ramos, M.J. Kerala, Índia: Transworld Research Network, 2008.
Edição de número de revista
  1. Sousa, Sérgio F.. "Modeling and Simulation of Enzymatic Catalysis Processes". Processes (2021): https://www.mdpi.com/journal/processes/special_issues/enzymatic_catalysis.
    Aceite para publicação • Editor convidado
  2. Sousa, Sérgio F.. "Structure and Function of Metalloenzymes". Molecules (2020): https://www.mdpi.com/journal/molecules/special_issues/structure_metalloenzymes.
    No prelo • Editor convidado
  3. Sousa, Sérgio F.. "The Application of Quantum Mechanics in the Reactivity of Molecules". Applied Sciences (2020): https://www.mdpi.com/journal/applsci/special_issues/Appl_Quantum_Mechanics.
    Aceite para publicação • Editor convidado
  4. Simoes, Manuel; Sousa, Sérgio F.; Giaouris, Efstathios. "Biofilm Control". Molecules (2020): https://www.mdpi.com/journal/molecules/special_issues/Biofilm_Control.
    No prelo • Editor convidado
  5. Sousa, Sérgio F.; Simoes, Manuel; Filipovic, Nenad. "The Chemistry of Biofilms and Their Inhibitors". Frontiers in Chemistry (2020): https://www.frontiersin.org/research-topics/9949/the-chemistry-of-biofilms-and-their-inhibitors.
    No prelo • Editor convidado
Poster em conferência
  1. Novais, Cláudia; Sousa, Sérgio F.; Abreu, Rui M.V.; Santos-Buelga, Celestino; Pereira, Carla. Autor correspondente: Pereira, Carla. "Exploring Molecular Dynamics for the Development of Bio-based Hybrid Molecules With Applications in Coloring and Preservation". Trabalho apresentado em International Conference on Sustainable Foods, 2024.
  2. Martins, Fábio G.; Sousa, Sérgio F.. "Optimizing Doxorubicin Delivery in Cancer Treatment with Lysinated Multiwalled Carbon Nanotubes: A Molecular Dynamics Study". Trabalho apresentado em Encontro Ciência 2024, 2024.
  3. Sousa, Sofia M.; Proença, Fernanda; Costa, Marta; Sousa, Sérgio F.. "KDM4C epigenetic therapy for triple-negative breast cancer". Trabalho apresentado em Encontro Ciência 2024 - Science and Technology Summit, 2024.
  4. Martins, Fábio G.; Sousa, Sérgio F.. "Molecular Dynamics Simulatons of Lysinated Multwalled Carbon Nanotubes for Enhanced Delivery of Doxorubicin in Cancer Therapy". Trabalho apresentado em 6th Meeting in Medicinal Biotechnology, 2024.
  5. Sousa, Sofia M.; Proença, Fernanda; Costa, Marta; Sousa, Sérgio F.. "Design of new epigenetic inhibitors for the treatment of triple negative breast cancer". Trabalho apresentado em 6th Meeting of Medicinal Biotechnology, 2024.
  6. Sousa, Sofia M.; Proença, Fernanda; Costa, Marta; Sousa, Sérgio F.. "Therapeutic epigenetic KDM4C remodeling for the treatment of triple negative breast cancer". Trabalho apresentado em 30th Porto Cancer Meeting, 2024.
  7. Margarida Cardeano Pinheiro; Mariana Fernandes; Sousa, Sérgio F.; Pratas, Diogo; Carneiro, João. "Decoding the Genomic Diversity of Hepatitis E Virus in European Rabbits: A Step Towards Understanding Zoonotic Transmission". Trabalho apresentado em The 20th Portugaliæ Genetica: DNA - Ancient and New 21-22 March 2024, 2024.
  8. Clara Cerqueira; Margarida Cardeano Pinheiro; Sousa, Sérgio F.; Pratas, Diogo; Carneiro, João. "Evolutionary Insights into Plastic-Degrading Enzymes: A Data-Driven Approach to Bioremediation". Trabalho apresentado em The 20th Portugaliæ Genetica: DNA - Ancient and New 21-22 March 2024, 2024.
  9. Mariana Fernandes; Clara Cerqueira; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. "Exploring the Evolution of PET-Degrading Enzymes: Insights from Sequence Alignment and Phylogenetic Analysis". Trabalho apresentado em The 20th Portugaliæ Genetica: DNA - Ancient and New 21-22 March 2024, 2024.
  10. Clara Cerqueira; E11D-C109-D995; Sousa, Sérgio F.; Pratas, Diogo; Carneiro, João. "Creating a Comprehensive Database of Plastic Degrading Enzymes for Machine Learning Applications". Trabalho apresentado em Bioinformatics Open Days XIII Edition 14-16 March 2024, 2024.
  11. Mariana Fernandes; Clara Cerqueira; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. "Unifying Information on Plastic Degrading Enzymes Across Different Databases". Trabalho apresentado em Bioinformatics Open Days XIII Edition 14-16 March 2024, 2024.
  12. Ana I. Furtado; Sousa, Sérgio F.; Vasco D.B. Bonifácio; Viveiros, R.; Casimiro, T.. "Rational design of ScCO2–assisted Bio–Molecularly Imprinting Polymers". Trabalho apresentado em 1st WG2 Virtual meeting of the COST COSY Action – "From quantum to classical dynamics of isolated molecules and 3D materials", February 6th, 2024.
  13. Mendes, Filipa; Cátia Santos-Pereira; Vieira, Tatiana F.; Martins-Pinto Mélanie; Castro, Bruno B.; Sousa, Sérgio F.; Sousa, Maria João; Devin Anne; CHAVES, SUSANA. "The cymoxanil fungicide impairs Saccharomyces cerevisiae respiration via complex IV inhibition". Trabalho apresentado em I CBMA Open Day & II PhD|Bio Symposium, 2024.
  14. Sousa, Sofia M.; Proença, Fernanda; Costa, Marta; Sousa, Sérgio F.. "Virtual screening of potential KDM4C inhibitors for the treatment of triple negative breast cancer". Trabalho apresentado em XXVII Encontro Luso-Galego de Química, 2023.
  15. Sousa, Sofia M.; Proença, Fernanda; Costa, Marta; Sousa, Sérgio F.. Autor correspondente: Sousa, Sofia M.. "Development of virtual screening protocols for the design of novel KDM4C inhibitors for the treatment of triple negative breast cancer". Trabalho apresentado em III ASPIC-ASEICA International Meeting – Cancer Immunology, Tumor Microenvironment and Metastasis, 2023.
  16. Sousa, Sofia M.; Proença, Fernanda; Costa, Marta; Sousa, Sérgio F.. "Optimization of specialized virtual screening protocols for the design of new KDM4C inhibitor molecules for the treatment of triple negative breast cancer". Trabalho apresentado em 5th National Meeting for Young Researchers in Oncology, 2023.
  17. Sousa, Sofia M.; Proença, Fernanda; Costa, Marta; Sousa, Sérgio F.. "Otimização de protocolos especializados de virtual screening para o design de novas moléculas inibidoras da KDM4C para o tratamento do cancro da mama triplo negativo". Trabalho apresentado em 5º Encontro Nacional de Jovens Investigadores em Oncologia, 2023.
  18. Mendes, Filipa; Cátia Santos-Pereira; Vieira, Tatiana F.; Martins-Pinto Mélanie; Castro, Bruno B.; Sousa, Sérgio F.; Sousa, Maria João; Chaves Susana R.. "Cymoxanil inhibits respiration through inhibition of mitochondrial complex IV". Trabalho apresentado em 31st International Conference on Yeast Genetics and Molecular Biology, 2023.
  19. Novais, Cláudia; Sousa, Sérgio F.; Abreu, Rui M.V.; Santos-Buelga, Celestino; Pereira, Carla. "Proposal for the Development of Bio-Based Hybrid Molecules: Exploring Molecular Dynamics for Coloring and Preservation of Molecules". Trabalho apresentado em Encontro com a Ciência e Tecnologia em Portugal (Encontro Ciência `23), 2023.
  20. Martins, Fábio G.; Fernandes, Henrique; Magalhães, Rita P.; Vieira, Tatiana F.; Sousa, Sérgio F.. "Computer-Guided Development of New Drugs Against COVID-19". Trabalho apresentado em 3D-BioInfo-PT Meeting, 2022.
  21. Martins, Fábio G.; Fernandes, Henrique; Magalhães, Rita P.; Vieira, Tatiana F.; Sousa, Sérgio F.. "Computer-Guided Development of Novel Drugs Against SARS-CoV-2". Trabalho apresentado em Medicinal Biotechnology // 5th Meeting and 2nd Iberian Congress, 2022.
  22. Shiraishi, C. S. H.; Sousa, Sérgio F.; Miguel Angel Prieto; Barros, Lillian; Abreu, Rui M.V.. "Virtual screening of a livrary of natural compounds against COX-2 protein". Trabalho apresentado em Biovia Conference, 2022.
  23. Vieira, Tatiana F.; Sousa, Sérgio F.. "Inverted Virtual Screening Approaches for the Identification of Protein Targets for Biologically Active Molecules". Trabalho apresentado em 5th Meeting of Medicinal Biotechnology (5MBtM) and 2nd Iberian Congress on Medicinal Biotechnology (2ICMBt), 2022.
  24. Martins, Fábio G.; Vieira, Tatiana F.; Moreira, Joel P.; Barbosa, Tiago; Sousa, Sérgio F.. "Specialized Multi-Level Computational Protocol for the Identification of Potential New Drugs". Trabalho apresentado em Encontro de Jovens Investigadores em Biologia Computacional Estrutural 2021, 2021.
  25. Pina, André F.; Sousa, Sérgio F.; Cerqueira, Nuno. Autor correspondente: Pina, André F.. "A computational study on the catalytic mechanism of Pdx2: a glutaminase containing the Cys-His-Glu triad". Trabalho apresentado em 8º Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE), 2021.
  26. Rita P. Magalhães; Victor de La Oliva; Carneiro, João; Sousa, Sérgio F.. "Optimization of Classification Models for Identification of Ligand-Target Inhibition Pairs in Biofilm Formation in P. aeruginosa". Trabalho apresentado em Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE), 2021.
    10.13140/RG.2.2.26841.39526
  27. Martins, Fábio; Melo, André; Sousa, Sérgio F.. Autor correspondente: Martins, Fábio. "Specialised Multi-Level Computational Approach For The Identification of Novel Quorum Sensing Inhibitors". Trabalho apresentado em EMBO: Advances and Challenges in Biomolecular Simulations Workshop, 2021.
  28. Vieira, Tatiana F.; Magalhães, Rita P.; Sousa, Sérgio F.. "In silico methodology for the identification of new drugs against biofilm formation in P. aeruginosa". Trabalho apresentado em The 24th meeting of the International Society for Molecular Recognition, Affinity 2021, 2021.
  29. Vieira, Tatiana F.; Sousa, Cristina E. A.; Sousa, Sérgio F.. "A Multi-Level Computational Approach in the Discovery of New Quorum Sensing Inhibitors for P. aeruginosa". Trabalho apresentado em Affinity 2021 Meeting, 2021.
  30. Dulce Quelhas; M. Martins; Carneiro, João; Jaeken, J.; Sousa, Sérgio F.; Azevedo, Luísa. "Effects of PMM2 single and double variants on protein stability and substrate interaction". Trabalho apresentado em Scientific CDG Symposium - Virtual Symposium 23-24 June 2021, 2021.
  31. Rita P. Magalhães; Tatiana F. Vieira; André Melo; Sousa, Sérgio F.. "Large Scale Virtual Screening for the Identification of new Drugs Against P.aeruginosa". Trabalho apresentado em BioExcel’s Remote Winter School on Biomolecular Simulations, 2020.
  32. Pina, André F; Sousa, Sérgio F.; Carneiro, J. "3D prediction of non-B DNA conformations associated with mtDNA genomic instability". Trabalho apresentado em 19th Portugaliæ Genetica (Porto, Portugal), 2020.
  33. Vieira, Cláudia Tatiana Freitas; Magalhães, Rita P.; Fernandes, Henrique; Simões, Manuel; Sousa, Sérgio F.. "Development of a structural database to inhibit biofilm formation". Trabalho apresentado em 7º Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE), 2019.
  34. Fernandes, Henrique S.; Cerqueira, N.M.F.S.A.; Sousa, Sérgio F.. "Using a computational approach to enhance enzymes as industrial biocatalysts". Trabalho apresentado em 7º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, FCUL (Lisbon, Portugal), 2019.
  35. Magalhães, Rita P.; Vieira, Cláudia Tatiana Freitas; Melo, André S.; Sousa, Sérgio F.. "Comparing Different Scoring Functions for Docking and Virtual Screening against bacterial Quorum-Sensing Receptors". Trabalho apresentado em 7º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, FCUL (Lisbon, Portugal), 2019.
  36. Vieira, T. F.; Magalhães, Rita P.; Fernandes, Henrique S.; Simões, M.; Sousa, Sérgio F.. "Development of a structural database to inhibit bio¿lm formation". Trabalho apresentado em 7º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, FCUL (Lisbon, Portugal), 2019.
  37. Sousa, Cristina E. A.; Pereira, C.; Fernandes, Henrique S.; Cerqueira, N.M.F.S.A.; Sousa, Sérgio F.. "RDB-TS: Development of a Database for Storage of Transition State Structures for Organic Reactions". Trabalho apresentado em 7º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, FCUL (Lisbon, Portugal), 2019.
  38. Rocha, Juliana F.; Cerqueira, N.M.F.S.A.; Sousa, Sérgio F.. "Improving the Threonine Aldolase activity to produce beta-hydroxy-alpha-amino acids by computational means". Trabalho apresentado em 7º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, FCUL (Lisbon, Portugal), 2019.
  39. Veloso, Andreia D.; Fernandes, A. J. S.; Ferraria, A. M.; Botelho do Rego, A. M.; Oliveira, M. C.; Videira, R. A.; Cerqueira, N.M.F.S.A.; Sousa, Sérgio F.. "Computational approach to the structural elucidation of an Electrogenerated Hydrophilic Carbon Nanomaterial". Trabalho apresentado em 7º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, FCUL (Lisbon, Portugal), 2019.
  40. Santos-Pereira, C.; Rodrigues, L. R.; Corte-Real, M.; Cerqueira, N.M.F.S.A.; Sousa, Sérgio F.. "Computational approach to study the interaction between the milk protein lactoferrin and V-ATPase". Trabalho apresentado em 7º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, FCUL (Lisbon, Portugal), 2019.
  41. Pina, André F.; Sousa, Sérgio F.; Cerqueira, Nuno M. F. S. A.. "Pyridoxine/pyridoxamine 5'-phosphate oxidase: a computational study". Trabalho apresentado em 7º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, 2019.
  42. Vieira, Tatiana F.; Magalhães, Rita P.; Sousa, Sérgio F.. "Looking into Protein Targets from the Perspective of the Ligand". Trabalho apresentado em Target Validation using Genomics and Informatics (EMBL - Heidelberg, Germany), 2019.
  43. Magalhães, Rita P.; Vieira, T. F.; Melo, André S.; Sousa, Sérgio F.. "Optimization of an in silico Virtual Screening Protocol for the Identification of Biofilm Formation Inhibitors in LasR". Trabalho apresentado em XXV Encontro Galego-Português de Química (Santiago de Compostela, Spain), 2019.
  44. Sousa, Sérgio F.. "Simulating Enzymatic Mechanisms by QM/MM Methods". Trabalho apresentado em CECAM Workshop – Protein Simulations – Current State of the Art (Tel Aviv, Israel), 2019.
  45. Vieira, Tatiana F.; Magalhães, Rita P.; Sousa, Sérgio F.. "Discovery of Quorum Sensing Inhibitors against P. aeruginosa using Docking and Virtual Screening Strategies". Trabalho apresentado em BImBS 2019 – BioInformatics meets BioSimulations in protein and DNA studies: from theory to practice (Lugano, Switzerlanda), 2019.
  46. Pina, André S.; Cerqueira, N.M.F.S.A.; Sousa, Sérgio F.. "Application of Molecular Dynamics Simulations in the Study of the PLP synthase Macrocomplex". Trabalho apresentado em BImBS 2019 – BioInformatics meets BioSimulations in protein and DNA studies: from theory to practice, 2019.
  47. Biernacki, K.; Sousa, Sérgio F.; Gales, L.; Ramos, M. J.; Magalhaes, A.L.. "Dipeptide Nanopores. A Non-Equilibrium Molecular Dynamics Study". Trabalho apresentado em XXVI Encontro Nacional da Sociedade Portuguesa da Química (Porto, Portugal), 2019.
  48. Sousa, J. P. M.; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "QM/MM study of DszB reaction mechanism for the biodesulphurization of crude oil". Trabalho apresentado em XXVI Encontro Nacional da Sociedade Portuguesa da Química (Porto, Portugal), 2019.
  49. Vieira, Tatiana F.; Magalhães, Rita P.; Sousa, Sérgio F.. "Docking and Virtual Screening strategies for the identification of new drugs against biofilm formation and developmen". Trabalho apresentado em XI Summer Course in Medicinal Chemistry, FFUP (Porto, Portugal), 2019.
  50. Fernandes, Henrique S.; Sousa, Sérgio F.; Cerqueira, N.M.F.S.A.. "Enhancing the catalytic power of Serine Hydroxymethyltransferase to produce commercially valuable compounds". Trabalho apresentado em The 44th FEBS Congress (Krakow, Poland), 2019.
  51. Fernandes, Henrique S.; Sousa, Sérgio F.; Cerqueira, N.M.F.S.A.. "Enhancing the catalytic power of Serine Hydroxymethyltransferase to produce commercially valuable compounds". Trabalho apresentado em 19th FEBS Young Scientists’ Forum (Krakow, Poland), 2019.
  52. Vieira, Tatiana F.; Magalhães, Rita P.; Sousa, Sérgio F.. "Docking and Virtual Screening strategies for the identification of new drugs against biofilm formation and development". Trabalho apresentado em XI Summer Course in Medicinal Chemistry, FFUP (Porto, Portugal), 2019.
  53. Teixeira, Carla S. S.; Sousa, Sérgio F.; Cerqueira, N.M.F.S.A.. "Molecular dynamic simulations and QM/MM studies addressed to build an active Tryptophan Synthase model. A critical enzyme to treat tuberculosis". Trabalho apresentado em 6th IEEE Portuguese Meeting on Bioengineering (ENBENG 2019), ISEL (Lisbon, Portugal), 2019.
    10.1063/1.3108362
  54. Magalhães, Rita P.; Vieira, Tatiana F.; Melo, André S.; Sousa, Sérgio F.. "Development of Specialized Virtual Screening Protocols for Inhibition of Quorum Sensing". Trabalho apresentado em IJUP - Encontro de Investigação Jovem, Reitoria da Universidade do Porto, (Porto, Portugal), 2019.
  55. Teixeira, Carla S. S.; Sousa, Sérgio F.; Cerqueira, N.M.F.S.A.. "Unraveling the catalytic mechanism of Tryptophan synthase, a drug target against Mycobacterium tuberculosis". Trabalho apresentado em 6º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Faculdade de Medicina da Universidade do Porto (Porto, Portugal), 2018.
  56. Fernandes, Henrique S.; Sousa, Sérgio F.; Cerqueira, N.M.F.S.A.. "Is the 5,10methylenetetrahydrofolate cofactor synthesized through a non-enzymatic or enzymatic mechanism?". Trabalho apresentado em 6º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Faculdade de Medicina da Universidade do Porto (Porto, Portugal), 2018.
  57. Sousa, João; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Single vs Multi Conformational QM/MM approach for enzymatic catalysis: The case of study of the HBP Sdesulfinase from the 4S pathway". Trabalho apresentado em 6º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Faculdade de Medicina da Universidade do Porto (Porto, Portugal), 2018.
  58. Rocha, Juliana F.; Freitas, David S.; Noro, Jennifer; Teixeira, Carla S. S.; Sousa, Cristina E. A.; Sousa, Sérgio F.; Alves, Maria J.; Cerqueira, N.M.F.S.A.. "Combined experimental and computational studies devoted to the synthesis of 1,4-lactones". Trabalho apresentado em 6º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Faculdade de Medicina da Universidade do Porto (Porto, Portugal), 2018.
  59. Paiva, Pedro; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Exploring the Catalytic Mechanism of the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase". Trabalho apresentado em 6º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Faculdade de Medicina da Universidade do Porto (Porto, Portugal), 2018.
  60. Magalhães, Rita P.; Vieira, Cláudia Tatiana Freitas; Fernandes, Henrique S.; Melo, André S.; Simões, Manuel; Sousa, Sérgio F.. "Creation of a Structural Database for Inhibition of Biofilm Formation". Trabalho apresentado em 6º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Faculdade de Medicina da Universidade do Porto (Porto, Portugal), 2018.
  61. Pina, André F.; Sousa, Sérgio F.; Cerqueira, N.M.F.S.A.. "Application of QM/MM Methods in the Study of PNPOx". Trabalho apresentado em 6º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Faculdade de Medicina da Universidade do Porto (Porto, Portugal), 2018.
  62. Teixeira, Carla S. S.; Sousa, Sérgio F.; Cerqueira, N.M.F.S.A.. "Unraveling the catalytic mechanism of Tryptophan synthase, a drug target against Mycobacterium tuberculosis". Trabalho apresentado em 6º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Faculdade de Medicina da Universidade do Porto (Porto, Portugal), 2018.
  63. Vieira, Cláudia Tatiana Freitas; Magalhães, Rita P.; Sousa, Sérgio F.. "Evaluation of Different Scoring Functions for Docking and Virtual Screening against GPCR Drug Targets". Trabalho apresentado em 6º Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Faculdade de Medicina da Universidade do Porto (Porto, Portugal), 2018.
  64. Pina, André F; Sousa, Sérgio F.; Cerqueira, Nuno M. F. S. A.. "Computational studies addressed to the catalytic mechanism of PNPOx". Trabalho apresentado em UCIBIO Annual Meeting (Lisbon, Portugal), 2018.
  65. Teixeira, Carla S. S.; Sousa, Sérgio F.; Ramos, M. J.; Cerqueira, Nuno M. F. S. A.. "Computational studies addressed to the catalytic mechanism of Tryptophan Synthase. An emergent target for the treatment of tuberculosis". Trabalho apresentado em UCIBIO Annual Meeting (Lisbon, Portugal), 2018.
  66. Fernandes, Henrique S.; Ramos, M. J.; Sousa, Sérgio F.; Cerqueira, N.M.F.S.A.. "The catalytic mechanism of Serine Hydroxymethyltransferase: a drug target against Malaria". Trabalho apresentado em UCIBIO Annual Meeting (Lisbon, Portugal), 2018.
  67. Makurat, Samanta; Chomicz-Manka, Lidia; Neves, Rui P. P.; Sousa, Sérgio F.; Fernandes, P. A.; Wityk, P.; Wieczor, M.; Czub, J.; Rak, J.. "QM/MM ONIOM calculations for DNA damage by solvated electrons. Optimizing a methodology for the modeling of radiotherapy-induced lesions". Trabalho apresentado em 3rd Congress of Polish Biosciences BIO 2018 – Through interdisciplinary approach into new solutions, Gdansk, Poland, 2018.
    10.1109/ppid.2003.1200949
  68. Vieira, T.F.; Sousa, Sérgio F.; Peres, J.; Coelho, M.. "PEGylation of Temozolomide (TMZ): A Molecular Dynamics study". Trabalho apresentado em WATOC 2017 (Munich, Germany), 2017.
  69. Soares, Susana; García-Estévez, Ignacio; Ferrer-Galego, Raúl; Brás, Natércia F.; Brandão, Elsa; Silva, Mafalda Santos; Teixeira, Natércia; et al. "Interaction of human salivary proteins with food polyphenols". Trabalho apresentado em ARBRE-MOBIEU 2017, 2017.
  70. Paiva, P.; Sousa, Sérgio F.; Ramos, M. J.; Fernandes, P. A.. "A QM/MM study of human Malonyl-Acetyl Transferase". Trabalho apresentado em Dynapeutics (Donostia, Spain), 2016.
  71. Biernacki, K.; Sousa, Sérgio F.; Gales, L; Ramos, M. J.; Magalhaes, A.L.. "Gas Diffusion inside L-Leucine-L-Serine Dipeptide Nanopores. A non-equilibrium MD study". Trabalho apresentado em DSL2016-12th International Conference on Diffusion in Solids and Liquids (Split, Croatia), 2016.
  72. Biernacki, K.; Sousa, Sérgio F.; Gales, L.; Ramos, M. J.; Magalhaes, A.L.. "Diffusion of small gases inside dipeptide nanotubes. A Non Equilibrium Molecular Dynamics study". Trabalho apresentado em XXIV Encontro Nacional da Sociedade de Portuguesa de Química (Coimbra, Portugal), 2015.
  73. Vieira, T.F.; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Strategies for Improved Ligand/Decoy Discrimination in Virtual Screening of Large Databases for Drug Discovery". Trabalho apresentado em IJUP 2015 (Porto, Portugal), 2015.
  74. Vieira, Tatiana F.; Sousa, Sérgio F.. "Development of New Consensus Scoring Functions for Virtual Screening in Metalloproteins". Trabalho apresentado em 2º Simpósio de Química Medicinal da Universidade do Minho, 2015.
  75. Biernacki, K.; Sousa, Sérgio F.; Gales, L.; Ramos, M. J.; Magalhaes, A.L.. "Modelling L-leucyl-L-serine (LS) dipeptide nanotubes: a molecular dynamics study". Trabalho apresentado em 11.º Encontro Nacional de Química Fisica (Porto, Portugal), 2013.
  76. Neves, R. P. P; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "A Parameterization Scheme on Manganese Metalloproteins for Biomolecular Force-Fields". Trabalho apresentado em X Girona Seminar on Theoretical and Computational Chemistry for the Modeling of Biochemical Systems: From Theory to Application (Girona, Spain), 2012.
  77. Coimbra, J. T. S.; Sousa, Sérgio F.; Fernandes, P. A.; Rangel, M.; Ramos, M. J.. "Drug interaction with hydrated glycerophospholipid bilayers". Trabalho apresentado em EBSA Biophysics Course on: Membrane Biophysics & Lipid/Protein Interaction (Bordeaux-Lacanau, France), 2012.
  78. Coimbra, J. T. S.; Sousa, Sérgio F.; Fernandes, P. A.; Rangel, M.; Ramos, M. J.. "Conception of Glycerophospholipid Hydrated Bilayer Models through Computational Modeling". Trabalho apresentado em 3PYCheM, 3rd Portuguese Young Chemists Meeting (Porto, Portugal), 2012.
  79. Neves, R.P.P.; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Setting a New Biomolecular Force-Field: Parameterizing Manganese First Coordination Spheres from Metalloproteins". Trabalho apresentado em 3PYCheM, 3rd Portuguese Young Chemists Meeting (Porto, Portugal), 2012.
  80. Coimbra, J. T. S.; Sousa, Sérgio F.; Fernandes, P. A.; Rangel, M.; Ramos, M. J.. "New biomolecular force field: lipid components". Trabalho apresentado em IJUP 2012 (Porto, Portugal), 2012.
  81. Martins, S.; Sousa, Sérgio F.; Ramos, M. J.; Fernandes, P. A.. "Development of New Methods for the Calculation of Solvation Free Energies in Computer-Aided Drug Design". Trabalho apresentado em 2.º Encontro Nacional de Química Terapêutica (Coimbra, Portugal), 2011.
  82. Coimbra, J. T. S.; Sousa, Sérgio F.; Fernandes, P. A.; Rangel, M.; Ramos, M. J.. "Parameterization of Lipidic Components for Molecular Dynamics Simulations of Biomembranes". Trabalho apresentado em Theobio 2011 (Funchal, Madeira, Portugal), 2011.
  83. Pinto, J. G.; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Comparative Assessment of Theoretical Methods for the Determination of Geometrical Properties in Biological Copper Coordination Spheres". Trabalho apresentado em Theobio 2011 (Funchal, Madeira, Portugal), 2011.
  84. Coimbra, J. T. S.; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.; Rangel, M.. "New Architectures to Fight Infectious Diseases under a Computational Themed Perspective". Trabalho apresentado em Second Iberic Meeting on Medicinal Chemistry: G Protein-coupled Receptors and Enzymes in Drug Discovery (Porto, Portugal), 2011.
  85. Pinto, J. G.; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Characterization of Nickel Complexes for Biomolecular Simulations". Trabalho apresentado em IJUP 2011 – 4th meeting of young researchers at UP (Porto, Portugal), 2011.
  86. Coimbra, J.T.S.; Sousa, Sérgio F.; Fernandes, P. A.; Rangel, M.; Ramos, M. J.. "Computational studies of the interaction between phospholipid bilayers and potential New Drugs". Trabalho apresentado em IJUP 2011 – 4th meeting of young researchers at UP (Porto, Portugal), 2011.
  87. Hari Narayana Moorthy, N.S.; Sousa, Sérgio F.; Ramos, M. J.; Fernandes, P. A.. "Computer Aided Structural analysis for FTase inhibition, hERG and Toxicity of Arylthiophene derivatives as anticancer agents". Trabalho apresentado em 18th European Symposium on Quantitative Structure Activity Relationships (Rhodes, Greece), 2010.
  88. Martins, S.; Sousa, Sérgio F.; Ramos, M. J.; Fernandes, P. A.. "New Computational Methods to Calculate Drug-Receptor Binding Free Energies". Trabalho apresentado em IJUP 2010 - 3rd meeting of young researchers at UP (Porto, Portugal), 2010.
  89. Pinto, J. R.; Fonseca, A.; Encarnação, I. C.; Sousa, Sérgio F.; Fernandes, P.A.; Ramos, M. J.. "Systematic Development of Molecular Dynamics Parameters for the Computational Modelling of Farnesyltransferase Inhibitors". Trabalho apresentado em IJUP 2010 - 3rd meeting of young researchers at UP (Porto, Portugal), 2010.
  90. Encarnação, I. C.; Pinto, J. R.; Fonseca, A.; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Determination of Molecular Mechanical Parameters for the Description of Ribonucleotide Reductase Inhibitors in Molecular Dynamics Simulations". Trabalho apresentado em IJUP 2010 - 3rd meeting of young researchers at UP (Porto, Portugal), 2010.
  91. Fonseca, A.; Pinto, J. R.; Ribeiro, D.; Encarnação, I. C.; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Computational Parameterization of Cytochrome P450 inhibitors for Molecular Dynamics Simulations". Trabalho apresentado em IJUP 2010 - 3rd meeting of young researchers at UP (Porto, Portugal), 2010.
  92. Hari Narayana Moorthy, N.S.; Sousa, Sérgio F.; Fernandes, P.A.; Ramos, M. J.. "In silico Structural Feature Study of Piperidine Analogs as FTase Inhibitors in Cancer Therapy". Trabalho apresentado em Biovalley Life Sciences Week 2009 (Basel, Switzerland), 2009.
  93. Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "First-Principles Computational Enzymology and QM/MM Insights into the Study of the Farnesyltransferase Enzyme". Trabalho apresentado em Introduction to Gaussian 09 Workshop: Theory and Practice (Ulm, Germany), 2009.
  94. Valente, M.; Sousa, Sérgio F.; Magalhães, A.L.; Freire, C.. "Complexation of alkali metal cations by a poly-ethylene-glycol type podand in dichloromethane. A MD study". Trabalho apresentado em 9.º Encontro Nacional de Química-Física (Aveiro, Portugal), 2009.
  95. Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Theoretical Studies on the Catalytic Mechanism of the Farnesyltransferase Enzyme". Trabalho apresentado em Quantum Pharmacology – 30 years on. A Special Conference in Honor of Professor W. Graham Richards (Oxford, UK), 2006.
  96. Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.; Fernandes, P.A.. "Protein Farnesyltransferase: Catalytic Portrait of a Zn Enzyme – A Computational Approach". Trabalho apresentado em 8th European Biological Chemistry Conference (EUROBIC 8) (Aveiro, Portugal), 2006.
  97. Sousa, Sérgio F.; Fernandes, P. A.. "Theoretical Studies on Farnesyltransferase: A Paradoxical Zinc Enzyme". Trabalho apresentado em 4.º Encontro REQUIMTE (Fátima, Portugal), 2006.
  98. Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Solving the Catalytic Mechanism of the Puzzling Metallo-Enzyme Farnesyl transferase: DFT, ONIOM, and AMBER Studies". Trabalho apresentado em FEBS Advanced Course: Theoretical Modelling of Ligand Binding and Enzymatic Catalysis (Tromso, Norway), 2005.
  99. Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Computational Studies on Zinc Enzymes: The Farnesyltransferase Case". Trabalho apresentado em Biomolecular Simulations, Satellite Meeting of the International Biophysics Congress (Bordeaux, France), 2005.
  100. Sousa, Sérgio F.; Fernandes, P.A.; Ramos, M.J.. "Farnesyltransferase – Unveiling the Catalytic Mechanism of a Puzzling Enzyme: A Theoretical Study". Trabalho apresentado em Biomolecular Simulations: From Prediction to Practice (Dublin, Ireland), 2005.
  101. Sousa, Sérgio F.; Fernandes, P.A.; Ramos, M. J.. "The Carboxylate-Shift in FTase – Analysing an Intriguing Mechanistic Feature in a Puzzling Enzyme". Trabalho apresentado em The World of Biophysics, Joint 15th IUPAB and 5th EBSA International Biophysics Congress (Montpellier, France), 2005.
  102. Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Determination of 3 Sets of Parameters for the Molecular Modelling of the Farnesyltransferase Enzyme". Trabalho apresentado em The World of Biophysics, Joint 15th IUPAB and 5th EBSA International Biophysics Congress (Montpellier, France), 2005.
  103. Sousa, Sérgio F.; Fernandes, P.A.; Ramos, M.J. "Molecular Modeling of Protein Farnesyltransferase – Analyzing a Critical Mechanistic Paradox". Trabalho apresentado em Bio-Image Summer School (Paris, France), 2005.
  104. Sousa, Sérgio F.; Fernandes, P.A.; Ramos, M. J.. "Farnesyltransferase – Theoretical Study of an Enigmatic Enzyme". Trabalho apresentado em Quantum Chemistry Applied: From H3 to Catalysis. A Special Conference in Honor of Professor Per E. M. Siegbahn (Stockholm, Sweden), 2005.
  105. Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Protein Farnesyltransferase - Mechanistic Portrait of a Puzzling Enzyme". Trabalho apresentado em VIth European Symposium of the Protein Society (Barcelona, Spain), 2005.
  106. Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Farnesiltransferase: Modelação Molecular no Combate ao Cancro". Trabalho apresentado em 7.º Encontro Nacional de Química-Fisica (Porto, Portugal), 2005.
  107. Tamames, B.; Tamames, J; Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Análise de Comprimentos de Ligação Atípicos Zinco-Oxigénio em Proteínas". Trabalho apresentado em 7.º Encontro Nacional de Química-Fisica (Porto, Portugal), 2005.
  108. Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Farnesyltransferase: Theoretical Studies on Substrate Peptide Entrance: Thiol or Thiolate Coordination?". Trabalho apresentado em 3rd Portuguese-Spanish Biophysics Congress (Lisbon, Portugal), 2004.
  109. Sousa, Sérgio F.; Fernandes, P. A.; Ramos, M. J.. "Farnesiltransferase: Estudo Teórico da Esfera de Coordenação do Zinco: Evidências para um Mecanismo de Carboxylate-Shift". Trabalho apresentado em QUITEL 2004 - XXX Congresso Internacional de Químicos Teóricos de Expressão Latina (Porto, Portugal), 2004.
  110. Sousa, Sérgio F.; Fernandes, P.A.; Ramos, M.J.. "Theoretical Studies on Farnesyltransferase - A New Anti-cancer Target". Trabalho apresentado em 3.º Encontro REQUIMTE (Fátima, Portugal), 2004.
  111. Fonseca, R.; Sousa, Sérgio F.; Ramos, M. J.. "Theoretical Studies on Cytochromes P450". Trabalho apresentado em Modelling chemical reactivity: from gas-phase to solution and enzymes (Nancy, France), 2003.
  112. Ramos, M. J.; Fonseca, R.; Sousa, Sérgio F.; Melo, A. S.. "Theoretical Studies on Cytochrome P450 1A2". Trabalho apresentado em 17th Symposium of The Protein Society (Boston, USA), 2003.
Recurso online
  1. Clara Cerqueira; Mariana Fernandes; Joana Rocha; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. Plastizyme: a central Hub for plastic biodegradation research. 2024. https://ml3denzymeoptimization.jc-biotechaiteam.com/.
  2. Rafael Primo Vieira; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. AptaCom: Bridging aptamer knowledge. 2024. http://jc-biotechaiteam.com/AptaCom.
Resumo em conferência
  1. Boazinha, João Pedro; Carneiro, João; Cerqueira, Nuno M. F. S. A.; Sousa, Sérgio F.. "Creation of a 3D-Molecular Database of Voltage-gate Sodium Channels". Trabalho apresentado em 6th Meeting of Medicinal Biotechnology, Porto, 2024.
  2. Brito-da-Costa, AM; Carvalho, Mariana; Dinis-Oliveira, Ricardo Jorge; Madureira-Carvalho, Áurea; Sousa, Sérgio F.; Dias da Silva, Diana. "In vitro and in silico evaluation of psilocybin and psilocin’s interaction with CYP450 enzymes". Trabalho apresentado em III 1H-TOXRUN International Congress - Scientific Letters, Porto, 2024.
    Publicado • 10.48797/sl.2024.236
  3. Brito-da-Costa, AM; Carvalho, Mariana; Dinis-Oliveira, Ricardo Jorge; Madureira-Carvalho, Áurea; Sousa, Sérgio F.; Dias da Silva, Diana. "In vitro and in silico evaluation of 5-MeO-DMT, LSD, and mescaline’s interaction with CYP450 enzymes". Trabalho apresentado em III 1H-TOXRUN International Congress - Scientific Letters, Porto, 2024.
    Publicado • 10.48797/sl.2024.237
  4. Sousa, Sérgio F.. "Creation of a Structural Database for Inhibition of Biofilm Formation". 2018.
    10.3390/mol2net-04-06079
  5. Sousa, Sérgio F.. "Is the 5,10-methylenetetrahydrofolate cofactor synthesized through a non-enzymatic or enzymatic mechanism?". 2018.
    10.3390/mol2net-04-06004
  6. Sousa, Sérgio F.. "Development of computational tools to enhance the study of catalytic mechanisms". 2017.
    10.3390/mol2net-03-05073

Propriedade Intelectual

Pedido provisório de patente
  1. 2021. "Vincent Parissi, Sérgio F. Sousa, D. Lapaillere, O. Delelis, L. Meertens, S. Gallois-Montbrun, S. Routier - Pharmaceutical composition, its use as a drug and new compounds, especially for treating SARS-CoV-2 infection (submitted)".
    Protegido
  2. 2021. "Vincent Parissi, Sérgio F. Sousa, D. Lapaillere, O. Delelis, L. Meertens, S. Gallois-Montbrun, M. Teulade-Fichou, R. Lartia, G. Bordeau - Pharmaceutical composition, its use as a drug and new compounds, especially for treating SARS-CoV-2 infection (submitted)".
    Protegido
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2022/01/06 Computational Biochemistry Approaches in the Study of the Biophysics of Proteins and Enzymes (Presenter: Sérgio F. Sousa) Temas Atuais em Biofísica e Bionanosistemas
Universidade do Minho (Braga (Online), Portugal)
2021/12/21 Developed of Inverted Virtual Screening Approaches for the Identification of Protein Targets Associated to the Biological Activity of Specific Molecules (Presenter: Tatiana F. Vieira) VIII EJIBCE (Encontro de Jovens Investigadores de Biologia Computacional Estrutural)
Faculdade de Ciências e Tecnologia da Universidade de Coimbra (Coimbra, Portugal)
2021/12/07 Applying Computational Biochemistry Methods to Understand Nature: Going for the Atomic Level Perspective (Presenter: Sérgio F. Sousa) Cycle of seminars of the M. Sc. in Medicinal Biotechnology
Escola Superior de Saúde (Porto, Portugal)
2021/12/06 A multidisciplinary approach to untangle the mechanisms behind the antifungal activity of lactoferrin (Presenter: Cátia Santos-Pereira) 15th International Conference on Lactoferrin: Structure, Function and Applications
(Beijing (Online), China)
2021/10/14 The Nitrate and Nitrite Reductase Activity of Xanthine Oxidase: a Computational Study (Presenter Henrique S. Fernandes) XXI SPB National Congress of Biochemistry
Universidade de Évora (Évora (Online), Portugal)
2021/10/07 Identification of potential quorum sensing inhibitors through structure-based virtual screening, molecular dynamics, and free energy calculations (Presenter: Fábio G. Martins) e-Conference on Innovation in Microbial Control
Univ Porto (Porto, Portugal)
2021/10/07 Targeting the PQS system: Discovery of New Quorum Sensing Inhibitors for P. aeruginosa through an in silico methodology (Presenter: Tatiana F. Vieira) e-Conference on Innovation in Microbial Control
Univ Porto (Porto, Portugal)
2021/10/07 Machine Learning Classification Models for Identification of Ligand-Target Inhibition Pairs in Biofilm Formation in P.aeruginosa (Presenter: Rita P. Magalhaes) e-Conference on Innovation in Microbial Control
Univ Porto (Porto, Portugal)
2021/10/07 Structure-based computational approaches targeting the inhibition of biofilm formation (Presenter: Sérgio F. Sousa) 1st E-Conference on Innovation in Microbial Control
FEUP (Porto, Portugal)
2021/10/01 Exploring the Nitrate and Nitrite Reductase Activity of Xanthine Oxidase – a QM/MM study (Presenter: Henrique S. Fernandes) 12th Molybdenum and Tungsten Enzymes Conference (MoTEC 2021)
(Marseille, França)
2021/07/21 Using Biomolecular Simulations to¿ Understand the Enzymatic Activity of Xanthine Oxidase (Presenter: Henrique S. Fernandes) BioSeminars@UCIBIO
UCIBIO (Lisboa, Portugal)
2021/06/22 Specialized multi-level computational approach for the identification of novel quorum sensing inhibitors (Presenter: Fábio G. Martins) 24th meeting of the International Society for Molecular Recognition, Affinity 2021
Univ Nova de Lisboa (Lisboa, Portugal)
2021/05/07 Structure-based Virtual Screening,Molecular Dynamics and Free Energy calculations for the identification of New Quorum Sensing Inhibitors (Presenter: Fábio G. Martins) Encontro de jovens investigadores da Universidade do Porto (IJUP)
Univ Porto (Porto, Portugal)
2021/05/07 Integrating Bioinformatics and Computational Chemistry in the search for Inhibitors of Bacterial Biofilm Formation (Presenter: Sérgio F. Sousa) First Webinar Series on Medicinal Chemistry - Designing Tomorrow’s Therapeutics
FCUP (Porto, Portugal)
2021/05/06 Deciphering the interaction of lactoferrin with V-ATPase towards a deeper understanding of its mechanisms of action (Presenter Cátia Santos-Pereira) X Bioinformatics Open Days
Univ Minho (Braga, Portugal)
2021/05/06 Structure-based Virtual Screening, Molecular Dynamics and Free Energy calculations for the identification of novel inhibitors against biofilm formation by C.violaceum (Presenter: Fábio Martins) X Bioinformatics Open Days
Univ Minho (Braga, Portugal)
2021/01/05 Computational Biochemistry Approaches in the Study of the Biophysics of Proteins and Enzymes (Presenter: Sérgio F. Sousa) Temas Atuais em Biofísica e Bionanosistemas
Universidade do Minho (M.Sc. in Biophysics and Bionanosystems) (Braga, Portugal)
2020/11/25 The Application of Computational Simulations in Teaching and Research in Chemistry (Presenter: Sérgio F. Sousa & Henrique S. Fernandes) Semana Acadêmica de Ciência e Tecnologia | V Semana Acadêmica de Química
Instituto Federal da Rondônia, Brazil (Rondônia, Brasil)
2020/11/17 Computational Chemistry in Drug Discovery (Presenter: Sérgio F. Sousa) Drug Research Webinar Series - Doctoral Programme in Drug Research
FinPharmaNet, University of Helsinki (Helsinki, Finlândia)
2020/09/30 Large Database Screening for the Identification of New Drugs Against Biofilm Formation in P.aeruginosa: a Computational Approach (Presenter Rita P. Magalhaes) Virtual EUGLOH Annual Students Research Conference on “Global Health Challenges: Diseases of Modern Life”
University of Szeged (Szeged, Hungria)
2020/03/05 Lead to Target: A Computational Approach to Identify Possible Protein Targets of Molecules with Known Experimental Biological Activity (Presenter: Sergio F. Sousa) MuTaLig COST Action CA15135
(Izmir, Turquia)
2020/01/15 Lead to Target: A Computational Approach to Identify the Protein Targets of Molecules with Known Experimental Biological Activity (Presenter: Sergio F Sousa) 13º Encontro Nacional de Química Orgânica / 6º Encontro Nacional de Química Terapêutica
Sociedade Portuguesa de Química (Aveiro, Portugal)
2019/12/16 Simulating Biomolecules with MD and QM/MM models with Fixed Point-Charges vs Polarizable Charges: Evolve or Wait? (Presenter: Sergio F. Sousa) CECAM Workshop “Beyond point charges: novel electrostatic developments in force fields”
CECAM (Lausanne, Suiça)
2019/12/08 Looking into Protein Targets from the Perspective of the Ligand (Presenter: Sergio F. Sousa) Target Validation using Genomics and Informatics
EMBL (Heidelberg, Alemanha)
2019/11/22 Application of Quantum Mechanics in The Study of Enzymatic Mechanisms (Presenter: Sergio F. Sousa) 2nd Quantum International Frontiers Meeting
University of Shanghai (Shanghai, China)
2019/11/15 BioSIM AR – Desenvolvimento de um Software Gratuito de Realidade Aumentada para o Ensino da Química (Presenter: Sergio F. Sousa) Encontro do Ensino e Divulgação da Química 2019
Sociedade Portuguesa de Química (Coimbra, Portugal)
2019/10/22 Simulating Enzymatic Mechanisms by QM/MM Methods (Presenter: Sergio F. Sousa) CECAM Workshop – Protein Simulations – Current State of the Art
CECAM - Israel Node (Tel Aviv, Israel)
2019/09/05 Molecular Dynamics Simulations in Modeling Biomolecular Systems (Presenter: Sergio F. Sousa) 2019 International Summer School in Computational Biology
CNC, University of Coimbra (Coimbra, Portugal)
2019/07/02 BioSIM - Employing Biomolecular Simulations in a Multidisciplinar Perspective (Presenter: Sergio F. Sousa) 6th BiotechHealth Symposium
Biotech Health Annual Symposium , I3S (Porto, Portugal)
2019/05/22 Da Mecanica Quantica às Simulações Atomísticas: Utilização do Computador no Estudo de Alvos Terapéuticos e da Reactividade Enzimática (Presenter: Sergio F. Sousa) Seminários FMUP
Faculdade de Medicina da Universidade do Porto (Porto, Portugal)
2019/05/19 Docking and Virtual Screening Application in Drug Development (Presenter: Sergio F. Sousa) Ciclo de Seminários, M.Sc. in Chemistry and Biochemistry, Course: Bioinformatics
Prof. André S. Melo, FCUP (Porto, Portugal)
2019/02/25 Docking and virtual screening application for drug development (Presenter: Sergio F. Sousa) PDBEB Courses 2018/2019 - Computational biology
CNC, University of Coimbra (Cantenhede, Portugal)
2018/05 Biomolecular Simulations at the Interface of Chemistry, Biochemistry, and Medicine (Presenter: Sergio F. Sousa) FMUP Seminars
FMUP (Portugal, Portugal)
2017/05 Making the Use of Protein-Ligand Docking in Drug Discovery More Effective (Presenter: Sergio F. Sousa) 3rd Symposium em Química Medicinal
(Braga, Portugal)
2016/06 How Enzymes Work: A Computational Approach (Presenter: Sergio F. Sousa) XII Encontro Nacional de Química-Física - Simpósio de Química Computacional
(Évora, Portugal)
2015/06 Improving Receptor-Ligand Scoring for Virtual Screening (Presenter: Sergio F. Sousa) XXIV Encontro Nacional da Sociedade Portuguesa de Química
(Coimbra, Portugal)
2015/05 Comparison of the Performance of AutoDock, Vina and GOLD in discriminating between Active Compounds and Decoys in Virtual Screening (Presenter: Sergio F. Sousa) 2.º Simposium em Química Medicinal
(Braga, Portugal)
2012/12 Comparative Assesment of Computational Methods for the Determination of Solvation Free Energies in Alcohol-based Molecules (Presenter: Sergio F. Sousa) XXXVIII Congresso of Theoretical Chemists of Latin Expression - Quitel
(Natal-RN, Brasil)
2012/05 Application of Computational Methods in the Clarification of Metal Coordination Spheres of Zinc Enzymes (Presenter: Sergio F. Sousa) CODECS COST Meeting Porto
(Porto, Portugal)
2011/07 Application of Computational Methods in the Determination of Physical Chemical Properties for Biomolecular Systems (Presenter: Sergio F. Sousa) XXII Encontro Nacional SPQ
(Braga, Portugal)
2011/06 Molecular Dynamics Applications on the Enzyme Farnesyltransferase (Presenter: Sergio F. Sousa) 5th Symposium on Theoretical Biophysics (TheoBio 2011)
(Madeira, Portugal)
2011/02 O uso de métodos de DFT no estudo de Metaloenzimas de Zn e os recentes progressos nesta área: uma perspectiva da química computacional (Presenter: Sergio F. Sousa) DFT@Portugal
(Coimbra, Portugal)
2011/01 Farnesyltransferase: a puzzling enzyme explained (Research Highlight) (Presenter: Sergio F. Sousa) 4.º Encontro REQUIMTE 2011
(Fátima, Portugal)
2010/10 Modelação Molecular de Novos Fármacos – O computador como ferramenta na procura de novos inibidores (Presenter: Sergio F. Sousa) 4.º Congresso Científico da Associação Portuguesa de Estudantes de Farmácia (APEF)
(Lisboa, Portugal)
2010/03 Computational Strategies for the Study of Membrane Translocation of Metal Atoms and of Metal Function and Reactivity Inside the cell (Presenter: Sergio F. Sousa) COST Meeting Action CM0902: Molecular machineries for ion translocation across biomembranes
(Hofheim am Taunus, Frankfurt, Alemanha)
2009/10 The Zinc Proteome – A Bioinformatics and Computational Chemistry View (Presenter: Sergio F. Sousa) 8th Inorganic Chemistry Conference (SPQ)
(Curia, Portugal)
2009/06 The Search for the Mechanism in the Reaction Catalyzed by the Enzyme Farnesyltransferase (Presenter: Sergio F. Sousa) 4th Symposium on Theoretical Biophysics (TheoBio-09)
(Roscoff, França)
2009/06 Computational Studies on Farnesyltransferase - Atomic Level Portrait of a Puzzling Enzyme (Presenter: Sergio F. Sousa) 9.º Encontro Nacional de Química-Física (SPQ)
(Aveiro, Portugal)
2007/06 The Search for the Mechanism in the Reaction Catalyzed by the Enzyme Farnesyltransferase (Presenter: Sergio F. Sousa) 3rd Symposium on Theoretical Biophysics (TheoBio-07)
(Cetraro, Itália)
2006/07 Protein Farnesyltransferase: Catalytic Portrait of a Zn Enzyme – A Computational Approach (Presenter: Sergio F. Sousa) 8th European Biological Chemistry Conference (EUROBIC 8)
(Aveiro, Portugal)
2005/10 Solving the Catalytic Mechanism of the Puzzling Metallo-Enzyme Farnesyl transferase: DFT, ONIOM, and AMBER Studies (Presenter: Sergio F. Sousa) FEBS Advanced Course: Theoretical Modelling of Ligand Binding and Enzymatic Catalysis
(Tromso, Noruega)

Orientação

Título / Tema
Papel desempenhado 		Curso (Tipo)
Instituição / Organização
2022/12/01 - Atual Epidemiological, Molecular and Biochemical aspects of Paroxysmal Nocturnal Hemoglobinuria
Coorientador de Vanda Patrícia Pinto Peixoto
 Pharmaceutical Sciences (Doutoramento)
Universidade de Vigo, Espanha
2022/10/01 - Atual Avaliação da toxicidade hepática aguda e inflamação induzida por nitrosaminas em Mus musculus e Danio rerio
Coorientador de Isabelly Annunciato
 Biodiversidade Costeira (Mestrado)
Universidade Estadual Paulista Júlio de Mesquita Filho - Câmpus do Litoral Paulista, Brasil
2022/09/01 - Atual Novel KDM4C inhibitors for the treatment of triple negative breast cancer: rational design, synthesis and biological validation
Coorientador de Sofia Isabel Martins de Sousa
 Health Sciences (Doutoramento)
Universidade do Minho, Portugal
2022/01/01 - Atual LFcin Refinery – Transforming a crude peptide sequence into valuable antimycobacterial products
Coorientador de Jorge Gabriel de Sousa Oliveira
 Biotecnologia Molecular e Celular Aplicada às Ciências da Saúde (Doutoramento)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2021/11/01 - Atual Rational Development of Nanomedicines for Cardiovascular Diseases
Orientador de Fábio António Gouveia Ferreira Martins
 Programa Doutoral em Biomedicina (Doutoramento)
Universidade do Porto Faculdade de Medicina, Portugal
2021/04 - Atual Development of machine learning algorithms for rational protein engineering [Interrupted]
Orientador de Carlos Pereira
 Programa Doutoral em Química Sustentável (Doutoramento)
REQUIMTE LAQV Porto, Portugal
2020/10/01 - Atual Development of new Heterocycle Structures inspired on Clozapine (Main Supervisor: Fernanda Proença, Univ Minho)
Coorientador de Rodrigo Andrade
 M.Sc. in Medicinal Chemistry (Mestrado)
Universidade do Minho, Portugal
2020/10/01 - Atual Molecular modelling of natural compounds extracted from plants as new insecticide agents
Orientador de Maria Francisca Araújo
 Biofísica e Bionanossistemas (Mestrado)
Universidade do Minho, Portugal
2019 - Atual Development of biocidal formulations for effective biofouling control (Main Supervisor: Manuel Simoes; Other Supervisor: Fernanda Borges)
Coorientador de Susana Maria da Fonseca Fernandes
Programa Doutoral em Engenharia Química e Biológica (Doutoramento)
Universidade do Porto Faculdade de Engenharia, Portugal
2018/12/01 - Atual New Drugs Against Biofilm Formation and Development: a Computational and Experimental Approach
Orientador de Cláudia Tatiana Vieira
 Programa Doutoral em Biomedicina (Doutoramento)
Universidade do Porto Faculdade de Medicina, Portugal
2018/10/01 - Atual Innovative approach to fight tuberculosis and malaria targeting the extraordinary PLP synthase macromolecular complex
Coorientador de André Pina
 Programa Doutoral em Biomedicina (Doutoramento)
Universidade do Porto Faculdade de Medicina, Portugal
2018/10 - Atual Rational development of new biocatalysts for the production of Parkinson Disease drugs
Coorientador de Juliana Rocha
 Programa Doutoral em Biomedicina (Doutoramento)
Universidade do Porto Faculdade de Medicina, Portugal
2022/10/01 - 2023/07/24 Improving a Database of Cyanobacterial Bioactive Compounds  for Therapeutic Approaches in Human Diseases 
Coorientador de Renato Soares
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2020/10/01 - 2022/06/30 Computational Optimization of Biocatalysts for Plastic Biodegradation
Orientador de Rita P. Magalhães
 Biomedicina (Doutoramento)
Universidade do Porto Faculdade de Medicina, Portugal
2020/10/01 - 2022/02/09 Application of QM/MM for the study of enzymes involved in plastic degradation
Orientador de Jorge Cunha
 Biofísica e Bionanossistemas (Mestrado)
Universidade do Minho, Portugal
2018/09 - 2021/07/27 Computational studies addressed to PLP-dependent enzymes
Coorientador de Henrique Silva Fernandes
 Programa Doutoral em Química (Doutoramento)
Universidade do Porto Faculdade de Desporto, Portugal
2018/09 - 2021/07/26 Computational Studies addressed to multi-functional enzyme complexes
Coorientador de Carla Silvia Silva Teixeira
 Programa Doutoral em Química (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2019/10 - 2020/07/21 Improving the efficiency of the energy split approach to compute the energy of a very large molecular system (Main Supervisor: Alberto Proenca, UMinho - Eng Informatics)
Coorientador de Sara Alexandra da Silva Pereira
 Master in Informatics Engineering (Mestrado)
Universidade do Minho - Departamento de Engenharia Informática, Escola de Engenharia, Portugal
2017 - 2018 The Mechanism of Reduction of HMG-CoA Catalyzed by Human HMG-CoA Reductase (Main Supervisor: Sérgio F. Sousa)
Orientador de Paula Mihaljevic-Juric
 Master in Chemistry (Mestrado)
UCIBIO@REQUIMTE, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Portugal

Organização de evento

Nome do evento
Tipo de evento (Tipo de participação) 		Instituição / Organização
2019/06/06 - 2019/06/07 Workshop de “Simulação Computacional de Biomoléculas” - a two-day workshop on biomolecular simulations, including molecular dynamics, molecular docking & virtual screening, and quantum chemistry calculations. (2019/06/06 - 2019/06/07)
Oficina (workshop) (Outra)
 Universidade de Trás-os-Montes e Alto Douro Escola de Ciências da Vida e do Ambiente, Portugal
2018/12/21 - 2018/12/21 6º Encontro de Jovens Investigadores de Biologia Computacional Estrutural - EJIBCE2018 (2018/12/21 - 2018/12/21)
Encontro (Presidente da Comissão Organizadora)
 Universidade do Porto Faculdade de Medicina, Portugal
2018/07/10 - 2018/07/10 Workshop: “The Use of Molecular Simulation Software”, V International Meeting Casa das Ciências (2018/07/10 - 2018/07/10)
Oficina (workshop) (Outra)
 Casa das Ciencias, Portugal
2012/05/04 - 2012/05/08 COnvergent Distributed Environment for Computational Spectroscopy – European Cooperation in Science and Technology (CoDECS-COST) (2012/05/04 - 2012/05/08)
Oficina (workshop) (Membro da Comissão Organizadora)
 Universidade do Porto Faculdade de Ciências, Portugal
2011/06/08 - 2011/06/12 5th Symposium on Theoretical Biophysics - TheoBio 2011 (Funchal, Madeira, Portugal) (2011/06/08 - 2011/06/12)
Simpósio (Membro da Comissão Organizadora)
 Universidade do Porto Faculdade de Ciências, Portugal
2011/06 - 2011/06 5th Symposium on Theoretical Biophysics (TheoBio 2011) (2011/06 - 2011/06)
Congresso (Membro da Comissão Organizadora)
 Universidade do Porto Faculdade de Ciências, Portugal

Participação em evento

Descrição da atividade
Tipo de evento 		Nome do evento
Instituição / Organização
2019/09/02 - 2019/09/12 Lecturer of the Module: “Molecular Dynamics Simulations in Modelling Biomolecular Systems"
Outro
 2019 Summer School in Computational Biology
Universidade de Coimbra, Portugal
2019/02/25 - 2019/03/01 Lecturer of the Module: “Docking and virtual screening application for drug development”
Outro
 PDBEB Courses 2018/2019 - Computational biology
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
2011/09 - 2011/09 Lecturer of the Module "Molecular Dynamics Simulation in Modelling Biochemical Processes" - 6th Intensive Course – Master in Theoretical Chemistry and Computational Modelling, Valencia, Spain
Oficina (workshop)
 6th Intensive Course – Master in Theoretical Chemistry and Computational Modelling
Universitat de València, Espanha
2010/07/01 - 2010/07/31 Lecturer of the Module "Molecular Dynamics Simulation in Modelling Biochemical Processes"
Oficina (workshop)
 5th Intensive Course – Master in Theoretical Chemistry and Computational Modelling, Porto, Portugal
Universidade do Porto Faculdade de Ciências, Portugal
2007/12/10 - 2007/12/11 V E-Learning Workshop of the University of Porto - A 2-days Workshop organizded by the Gabinete de Apoio às Novas Tecnologias na Educação da Universidade do Porto (GATIUP), FADEUP - University of Porto, Porto
Oficina (workshop)
 V E-Learning Workshop of the University of Porto
Universidade do Porto - Gabinete de Apoio às Novas Tecnologias (GATIUP), Portugal
2006/04 - 2006/06 Intellectual Property and Technology Transfer, 24-hours Course Organised by the Instituto de Recursos e Iniciativas Comuns da UP (IRICUP) in Collaboration with Clarke, Modet & Co., Rectory of the University of Porto
Oficina (workshop)
 Intellectual Property and Technology Transfer
Universidade do Porto, Portugal
2005/02 - 2005/11 Entrepreneurship Course, 102-hours Course Organised by the EGP and Instituto de Recursos e Iniciativas Comuns da UP (IRICUP). Porto School of Management (EGP), University of Porto. Porto, Portugal
Oficina (workshop)
 Curso de Empreendedorismo
Universidade do Porto Porto Business School, Portugal
2005/10/16 - 2005/10/21 FEBS Advanced Course: Theoretical Modelling of Ligand Binding and Enzymatic Catalysis 6-Days Advanced Course, Norwegian Structural Biology Centre (NorStruct). Tromso, Norway
Oficina (workshop)
 FEBS Advanced Course:
Universitetet i Tromsø Nasjonalt senter for strukturbiologi, Noruega
2005/07/11 - 2005/07/22 Bio-Image Summer School - Paris2005, 2-Weeks Summer School on Manipulation, Visualization and Modeling of Single Molecules, École Normale Supérieure (ENS), Paris, France Bio-Image Summer School
École Normale Supérieure, França
2005/02/17 - 2005/02/17 Forensic Chemistry, 1-Day Workshop Organized by the Department of Chemistry, Faculty of Sciences of the University of Porto
Oficina (workshop)
 Forensic Chemistry
Universidade do Porto Faculdade de Ciências, Portugal
2005/01/22 - 2005/01/26 Second European School on Bioinformatics, 5-Days Course Organized by the Biosapiens Networks of Excellence. CMBI, Faculty of Science of the Radboud University Nijmegen, Nijmegen, The Netherlands
Oficina (workshop)
 Second European School on Bioinformatics
Radboud Universiteit Centre for Molecular and Biomolecular Informatics, Países Baixos
2004/09/09 - 2004/09/11 Solvation Methods in Quantum Chemistry, 3-hours Advanced Course presented by V. Barone, in QUITEL 2004, Faculty of Sciences of the University of Porto, Porto, Portugal
Oficina (workshop)
 Solvation Methods in Quantum Chemistry
Universidade do Porto Faculdade de Ciências, Portugal

Júri de grau académico

Tema
Tipo de participação 		Nome do candidato (Tipo de grau)
Instituição / Organização
2022/04 Targeting Neuroinflammation: From target validation to rational design of selective modulators
Arguente principal
 João Pedro dos Reis Luís (Doutoramento)
Universidade de Coimbra, Portugal
2022/03/04 Novel chromene and imidazole derivatives: Synthesis, biological evaluation and computational studies
Arguente principal
 Fábio Daniel Pedroso de Lima da Conceição (Doutoramento)
Universidade do Minho, Portugal
2022/02/09 Computational Development of New Biocatalyst for Plastic Degradation through QM/MM Methods
Orientador
 Jorge Miguel Fernandes da Cunha (Mestrado)
Universidade do Minho, Portugal
2021/11/18 Development of an antidote for Russell's viper (Daboia russelii russelii) venom factor X activating enzyme (RVV-X)
Arguente principal
 Juliana Amorim (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2021/11/02 Development of a new pharmacokinetic model usin in silico studies, drug delivery systems and analytical methods
Arguente
 Abigail Filipe Ferreira (Doutoramento)
Universidade do Porto Faculdade de Desporto, Portugal
2019/07 In Silico Identification and Characterization of 4 Novel Families of Potential Toxins in the Octocorallian Eunicella Singularis
Arguente
 Marco Oliveira (Outro)
Instituto Politécnico do Porto Escola Superior de Saúde, Portugal
2015 Development of a computational protocol to study passive diffusion through biological membranes
Arguente principal
 Rui Pedro Fernandes Ribeiro (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2015 New Computational Methods to Calculate Drug-Receptor Binding Free Energies
Vogal
 Silvia Alexandra Pinto Martins (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2014/07 The Van Der Waals Interactions in Graphitic Systems
Arguente
 Karol Strutynski (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2012/09 Determinação computacional dos efeitos da mutagénese em interfaces proteína-DNA
Arguente principal
 Rui Miguel De Castro e Ramos (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2012 Fractalidade em moléculas informacionais
Arguente
 Juan António Casas Tamames (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2012 Estudo Teórico do Mecanismo de Catálise Assistida pela Enzima ß-Hesosaminidase A
Arguente principal
 Óscar Abílio Leal Ferreira Passos (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2010/12/21 Computer-Aided Drug Design - Lead Discovery
Arguente
 João Rui Vieira Ribeiro (Outro)
Universidade do Porto Faculdade de Ciências, Portugal
2010 Estudo Teórico do Mecanismo de Catálise Assistida pela Enzima Beta-Hexosaminidase A
Arguente principal
 Diana Sofia Gesto Da Silva (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal

Arbitragem científica em conferência

Nome da conferência Local da conferência
2020/02/12 - 2020/02/14 IJUP2020 - Investigação Jovem na Universidade do Porto (Representative for Chemistry) University of Porto
2019/02/13 - 2019/02/15 IJUP2019 - Investigação Jovem na Universidade do Porto (Representative for Chemistry) University of Porto

Outro júri / avaliação

Descrição da atividade Instituição / Organização
2017 - 2017 Worked as Evaluator for the Agence Nationale de la recherche (ANR, France) as external expert Agence nationale de la recherche, França
2014 - 2014 Worked as Evaluator for the National Science Foundation (NSF / USA) as external expert National Science Foundation, Estados Unidos
2014 - 2014 Worked as Evaluator for the Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT, Argentina) as external expert Agencia Nacional De Promoción Científica Y Tecnológica, Argentina
2009 - 2009 Worked as Evaluator for the Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT, Argentina) as external expert Agencia Nacional De Promoción Científica Y Tecnológica, Argentina
Distinções

Outra distinção

2020 CEEC2020 Grant Award
Fundação para a Ciência e a Tecnologia, Portugal
2009 Prémio Estímulo à Investigação da Gulbenkian 2009
2007 2nd Most Acessed Paper - Journal of Physical Chemistry A
American Chemical Society, Estados Unidos
2005 2nd in the Best Poster Contest - 7ENQF (SPQ)
2003 Academic Award Eng. António de Almeida 2002/2003 - Highest Final Classification in the Chemistry Degree
Universidade do Porto Faculdade de Ciências, Portugal
2001 Academic Award Dr. Mendonça Monteiro 2000 / 2001 - Highest final average classification in the set of chairs of the Physical Chemistry Area in the Chemistry Degree
Universidade do Porto Faculdade de Ciências, Portugal