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2024

International articles with referee

  1. Melnik, T., Sinval, J., Pinho, V. D. de, Junior, J. A. S. H., Oliveira, M. da S., & Lopes, F. M. (2025). Knowledge and use of evidence-based practice in psychology in the clinical practice of Brazilian psychologists: A cross-sectional study. Healthcare, 13(4), 1–18. https://doi.org/10.3390/healthcare13040431
  2. Nevado B, Atchison GW, Bridges EL, Orzell S, Filatov D, Hughes CE. Pleistocene diversification of unifoliolate-leaved Lupinus (Leguminosae: Paplionoideae) in Florida. Molecular Ecology (accepted).
  3. Andrade, R., Laranjeiro, N., & Vieira, M. (2024). BugHub: A Large Scale Issue Report Dataset. In 19th European Dependable Computing Conference - EDCC, accepted for publication. Leuven.
  4. Sinval, J., Oliveira, P., Novais, F., Almeida, C. M., & Telles-Correia, D. (2024). Correlates of burnout and dropout intentions in medical students: A cross-sectional study. Journal of Affective Disorders. https://doi.org/10.1016/j.jad.2024.08.003
  5. "Leveraging LLMs for On-the-fly Instruction Guided Image Editing" dos autores Rodrigo Santos, João Silva e António Branco EPIA 2024, International Conference on Artificial Intelligence (https://doi.org/10.48550/arXiv.2403.08004)
  6. Morais, I., Carneiro, F. A., Sinval, J., Costa, P. A., & Leal, I. (2024). The Walsh Family Resilience Questionnaire: Validity evidence from Portugal. Family Relations. https://doi.org/10.1111/fare.13078
  7. Sinval, J., Oliveira, P., Novais, F., Almeida, C. M., & Telles-Correia, D. (2024). Exploring the impact of depression, anxiety, stress, academic engagement, and dropout intention on medical students’ academic performance: A prospective study. Journal of Affective Disorders. https://doi.org/10.1016/j.jad.2024.09.116
  8. Melo, L. E. A. de, Sinval, J., & Isler, C. A. (2025). Prospective avenues in travel behavior research supported by the cognitive dissonance theory: A scoping review. Transportation Research Part F: Traffic Psychology and Behaviour, 109, 501–519. https://doi.org/10.1016/j.trf.2024.12.022
  9. Galamba, N., Sickle Cell Hemoglobin “Drugged” with Cyclic Peptides is Aggregation Incompetent, J. Phys. Chem. B, 128, 36, 8662, 2024 URL: https://doi.org/10.1021/acs.jpcb.4c03805
  10. Martins, G., Galamba, N., Wild Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study, J. Chem. Inf. Model., 64, 15, 6115, 2024 URL: https://doi.org/10.1021/acs.jcim.4c00965
  11. Gomes I., Martins, G., Galamba N., Essential Dynamics of Ubiquitin in Water and in a Natural Deep Eutectic Solvent, Phys. Chem. Chem. Phys., 26, 18244, 2024 URL: htps://pubs.rsc.org/en/Content/ArticleLanding/2024/CP/D4CP01773K
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  12. Iana Lychko; Cátia Lopes Soares; Barbosa, A.J.M.; Tomás Rosa Calmeiro; Rodrigo Ferrão de Paiva Martins; Ana Margarida Gonçalves Carvalho Dias; Ana Cecília Afonso Roque. "Kinetics of charge-dependent reversible condensation of reflectin nanostructures". Materials Advances (2024): https://doi.org/10.1039/D4MA00788C.
  13. In silico identification of novel PqsD inhibitors: promising molecules for quorum sensing interference in Pseudomonas aeruginosa – Tatiana F. Vieira; Nuno M. F. S. A. Cerqueira; Manuel Simões; Sérgio F. Sousa – Molecular Systems Design & Engineering – 2024 – 10.1039/D3ME00107E
  14. The fungicide cymoxanil impairs respiration in Saccharomyces cerevisiae via cytochrome oxidase inhibition – Filipa Mendes; Cátia Santos-Pereira; Tatiana F. Vieira; Mélanie Martins Pinto; Bruno B. Castro; Sérgio F. Sousa; Maria João Sousa; Anne Devin; Susana Chaves – FEBS Letters – 2024 – 10.1002/1873-3468.14907
  15. Dual action of benzaldehydes: Inhibiting quorum sensing and enhancing antibiotic efficacy for controlling Pseudomonas aeruginosa biofilms – Miguel M. Leitão; Tatiana F. Vieira; Sérgio F. Sousa; Fernanda Borges; Manuel Simões; Anabela Borges – Microbial Pathogenesis – 2024 – 10.1016/j.micpath.2024.106663
  16. Montelukast and cefoperazone act as antiquorum sensing and antibiofilm agents against Pseudomonas aeruginosa – Tatiana F Vieira; Miguel M Leitão; Nuno M F S A Cerqueira; Sérgio F Sousa; Anabela Borges; Manuel Simões – Journal of Applied Microbiology – 2024 – 10.1093/jambio/lxae088
  17. In silico-guided discovery and in vitro validation of novel sugar-tethered lysinated carbon nanotubes for targeted drug delivery of doxorubicin – Fábio G. Martins; Chanchal Kiran Thakur; Chandrabose Karthikeyan; Subhasmita Bhal; Chanakya Nath Kundu; N. S. Hari Narayana Moorthy; Sérgio F. Sousa – Journal of Molecular Modeling – 2024 https://doi.org/10.1007/s00894-024-06061-5
  18. Protocol for in silico characterization of natural-based molecules as quorum-sensing inhibitors – Susana Fernandes; Mariana Sousa; Fábio G. Martins; Manuel Simões; Sérgio F. Sousa – STAR Protocols – 2024 – http://dx.doi.org/10.1016/j.xpro.2024.103367 1- Protocolo de Bioinformática para ensino de estrutura e função de proteínas. Roggero, A., Nicodemo, I., Annunciato, I., da Silva Fernandes, P. H., Mota, V., & Toyama, M. H. (2024). Revista de Ensino de Bioquímica, 22(2), 119-136. https://doi.org/10.16923/reb.v22i2.1088 1- Structural insights of an LCP protein–LytR–from Streptococcus dysgalactiae subs. dysgalactiae through biophysical and in silico methods - J Paquete-Ferreira, F Freire, HS Fernandes, J Muthukumaran, J Ramos, et al. Frontiers in Chemistry 12, 1379914, 2024 https://doi.org/10.3389/fchem.2024.1379914 Evaluation of the impact of two C5 genetic variants on C5-eculizumab complex stability at the molecular level - VP Peixoto, C Prudêncio, M Vieira, SF Sousa, Journal of Biomolecular Structure and Dynamics, 1-10, 2024, https://doi.org/10.1080/07391102.2024.2331091
  19. Exploiting Locusta migratoria as a source of bioactive peptides with anti-fibrosis properties using an in silico approach (vol 15, pg 493, 2024) CSS Teixeira, R Biltes, C Villa, SF Sousa, J Costa, IM Ferreira, I Mafra - FOOD & FUNCTION 15 (5), 2773-2773, https://doi.org/10.1039/D3FO04246D 1- Glucocorticoid receptor-dependent therapeutic efficacy of tauroursodeoxycholic acid in preclinical models of spinocerebellar ataxia type 3 - S Duarte-Silva, JD Da Silva, D Monteiro-Fernandes, MD Costa, SF Sousa et al. The Journal of clinical investigation 134 (5) (2024) 10.1172/JCI162246
  20. Substitution models of protein evolution with selection on enzymatic activity D Ferreiro, R Khalil, SF Sousa, M Arenas, Molecular Biology and Evolution 41 (2), 2024 msae026 https://doi.org/10.1093/molbev/msae026 1- Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for Therapeutics and Bioremediation - R Soares, L Azevedo, V Vasconcelos, D Pratas, SF Sousa, J Carneiro - Journal of Chemical Information and Modeling 64 (24), 9576-9593 https://doi.org/10.1021/acs.jcim.4c00995
  21. Advances in structure-based drug design targeting membrane protein markers in prostate cancer - Batista- Silva J.P., Gomes D., Sousa S.F., Sousa Â., Passarinha L.A. - Drug Discovery Today, 2024, 29(9): 104130 https://doi.org/10.1016/j.drudis.2024.104130
  22. Structural insights and photophysical properties of mononuclear and pentanuclear Zn(II) acetate complexes with pyridyl-based thiazolyl-hydrazones - Araškov J.B., Garcia-Sosa A.T., Višnjevac A., Sousa S.F., Holló B.B., Uğuz Ö., Koca A., Monge M., Rodríguez-Castillo M., López-de-Luzuriaga J.M., Todorović T.R., Filipović N.R. - Polyhedron, 2024, 262: 117162 https://doi.org/10.1016/j.poly.2024.117162 1- In silico analysis of aptamer-RNA conjugate interactions with human transferrin receptor Vasconcelos D., Pina A., Habib N., Sousa S.F. - Biophysical Chemistry, 2024, 314: 107308 https://doi.org/10.1016/j.bpc.2024.107308
  23. LC-ESI-UHR-QqTOF-MS/MS profiling and anti-inflammatory potential of the cultivated Opuntia ficus-indica (L.) Mill. and the wild Opuntia stricta (Haw.) Haw. fruits from the Algerian region - Zeghbib W., Boudjouan F., Carneiro J., Oliveira A.L.S., Sousa S.F., Pintado M.E., Ourabah A., Vasconcelos V., Lopes G. - Food Chemistry, 2024, 460: 140414 https://doi.org/10.1016/j.foodchem.2024.140414
  24. Design, synthesis, and pharmacological evaluation of heteroaryl thiol-linked kojic acid derivatives as a novel class of acetylcholinesterase inhibitors for Alzheimer’s disease therapy - Singh M., Karthikeyan C., Waiker D.K., Tiwari A., Shrivastava S.K., Sousa S.F., Kiriwan D., Martins F.G., Moorthy N.S.H.N. - 3 Biotech, 2025, 15(5): 134 https://doi.org/10.1007/s13205-025-04295-5
  25. A comprehensive update of genotype–phenotype correlations in PMM2-CDG: insights from molecular and structural analyses - Oliveira T., Ferraz R., Azevedo L., Quelhas D., Carneiro J., Jaeken J., Sousa S.F. - Orphanet Journal of Rare Diseases, 2025, 20(1): 207 https://doi.org/10.1186/s13023-025-03669-5 Design and biological evaluation of 2-phenylquinoxaline carbonyl piperazine derivatives as novel FASN inhibitors with anticancer activity - S Singh, S Paul, FG Martins, SF Sousa, CN Kundu, C Karthikeyan, - Bioorganic Chemistry, 2025, 10869 https://doi.org/10.1016/j.bioorg.2025.108697
  26. Two cinnamic acid derivatives as inhibitors of Pseudomonas aeruginosa las and pqs quorum-sensing systems: Impact on biofilm formation and virulence factors - MM Leitão, ASC Gonçalves, SF Sousa, F Borges, M Simões, A Borges, Biomedicine & Pharmacotherapy 2025, 187, 118090 https://doi.org/10.1016/j.biopha.2025.118090

Oral Presentations

  1. LFcin Refinery: A machine learning approach to improve antimicrobial peptides’ efficacy against nontuberculous mycobacteria Gabriel S. Oliveira, Maria Salomé Gomes, Sérgio F. Sousa, Tânia Silva - IMAP 2024 11th International Meeting on Antimicrobial Peptides 2024/09/02-04 (London, United Kingdom) 1- Tackling biofilm formation using an in silico approach Tatiana F. Vieira - LAQV Webinar 2024/04/17 (Porto, Portugal) (online)
  2. Exploring pH-dependent Dynamics Of Doxorubicin Delivery Using Functionalized Multi-walled Carbon Nanotubes: Insights From Molecular Dynamics Simulations Fábio G. Martins, Sérgio F. Sousa – Biophysics Festival - 4th Meeting of Young Biophysics 9-10.05.2024 (Covilhã, Portugal)
  3. Development of a Computational Protocol for the Rational Design of Nanomedicines Aimed at Cardiovascular Diseases Fábio G. Martins, Sérgio F. Sousa – XXII National Congress of Biochemistry 24-26.10.2024 (Aveiro, Portugal)
  4. Use of HPC Computing for Accelerating Drug Discovery Targeting the SARS-CoV-2 S-RDB/ACE2 Interaction Fábio G. Martins, Sérgio F. Sousa IBERGRID 2024 – 28-30.10.2024 (Porto, Portugal)
  5. A Computational Strategy for the Design of Targeted Nanomedicines in Cardiovascular Diseases Fábio G. Martins, Sérgio F. Sousa – XXVIII Encontro Galego-Português de Química 13-15.11.2024 (Vigo, Spain)
  6. Molecular Insights into HIV-1 Integration: A Computational Study of Intasome-Nucleosome Interactions Fábio G. Martins, Sérgio F. Sousa – LAQV WEBINAR 21.05.2025 (Online)
  7. Development and Application of a Multi-Level Computational and In Vitro Approach for Identifying MAPK3 Inhibitors in Leishmania martiniquensis and Leishmania orientalis – Duangnapa Kiriwan, Tatiana F. Vieira, Nutnaree Kumsiri, Kiattawee Choowongkomon, Sergio F. Sousa - BIOPHYSICS FESTIVAL – 4 th Meeting of Young Biophysicists - 9-10.05.2024
  8. Tripeptide-Based Inhibition of EGFR Tyrosine Kinase in Lung Cancer: Findings from Computational and Experimental Studies - Duangnapa Kiriwan, Supaphorn Seetaha, Nattanan Jiwacharoenchai, Lueacha Tabtimmai, Napat Songtawee, Kiattawee Choowongkomon, Sérgio F. Sousa - XXII SPB National Congress of Biochemistry - 24- 26.10.2024 1- From plants to anti-snakebite mechanisms. Airam Roggero, Isabelly Annunciato, Fabio G. Martins, Igor Nicodemo, Marcos H.Toyama, Sergio F. Sousa. 6th Meeting on Medicinal Biotechnology 2024
  9. Effects of Morin on Cell Membrane Fluidity: An Analysis of the Anti-inflammatory Efficacy of Flavonoids. Airam Roggero, Caroline Ramos da Cruz, Marcos H. Toyama, Sergio F. Sousa. - XXIX National Meeting of the Portuguese Chemical Society, Coimbra, Portugal, 2025.
  10. Enzyme Modulation and Inflammation: A New Therapeutic Target. Airam Roggero, Marcos H. Toyama, Sergio F. Sousa - 7th Symposium on Medicinal Chemistry of University of Minho, Braga, Portugal, 2025.
  11. Aspartame and Inflammation: An In Silico Evaluation of Interference in the Land’s Cycle and Cell Membrane Integrity. Isabelly Annunciato; Michelle Rafael; Igor Nicodemo; Airam Roggero; Caroline R. da Cruz; Mariana N. Belchor; Adeilso B. S. Junior; Gustavo A. Fernandes; Marcos A. de Oliveira; Sérgio F. Sousa; Marcos Hikari Toyama – XXVII Encontro Luso Galego de Química 22/11/2023 to 24/11/ 2023 (Porto, Portugal)
  12. Use of HPC Resources to Find New Drugs Against Biofilm Formation Tatiana F. Vieira, Sérgio F. Sousa - IBERGRID 2024 2024/10/28-30 (Porto, Portugal)
  13. Engineering aptamers for Biomedical Application using Biomolecular Simulations Sérgio F. Sousa - 26th Congress of the International Union of Biochemistry and Molecular Biology (IUBMB) 2024/09/25 (Melbourne, Australia)
  14. Development of Computational Methods For Aptamer Engineering For Targeted-Drug Delivery Sérgio F. Sousa - XXVIII EFMC International Symposium on Medicinal Chemistry 2024/09/03 (Rome, Italy) (Flash talk/poster)
  15. Application of QM/MM Methods in Enzyme Bioengineering Efforts: Understanding PET Degrading Activity of PETases Sérgio F. Sousa - XLVII International Congress of Theoretical Chemists of Latin Expression (Chitel2024) 2024/07/03 (Namur, Belgium)
  16. Application of QM/MM Methods in the Study of the Enzyme Efficiency by PET Degrading Enzymes Sérgio F. Sousa - ESPA2024 Meeting (Electronic Structure Principles and Applications Conference) 2024/06/06 (Tarragona, Spain)
  17. Probing the Role Played by Different Amino Acid Residues in the Catalytic Mechanism of Plastic PET Degrading Enzymes by QM/MM Methods Sérgio F. Sousa - International Society of Quantum Biology and Pharmacology (ISQBP) 2024 President’s Meeting 2024/05/21 (Athens, Greece)
  18. Towards One Health: Combining Biomolecular Simulations, Artificial Intelligence and Scientific Databases Sérgio F. Sousa - 1-day Course for the PhD Program in Integrated Health (One Health) at FMUP (Invited Lecture) 2024/11/15 – (Porto, Portugal)
  19. Development of Multi-Level Biomolecular Simulation Protocols for Aptamer Engineering for Biomedical Applications Sérgio F. Sousa - 13th Iberian Grid Conference – IBERGRID 2024 (Plenary Lecture) 2024/10/30 – (Porto, Portugal)
  20. Application of QM/MM Methods in Enzyme Bioengineering Efforts: Understanding PET Degrading Activity of PETases Sérgio F. Sousa - International Symposium on Future in Enzyme Modeling (FEM2024) (Invited lecture) 2024/10/25 – (Tianjin, China)
  21. Combining Biomolecular Simulations with Medicinal Chemistry: Expanding Horizons Sérgio F. Sousa - Global Health Horizons: Empowering Pharmacists Through Research and Development Conference - World Pharmacists Day 2024 - Indira Gandhi National Tribal University (Plenary Lecture) 2024/09/24 – (Amarkantak, Madhya Pradesh, India) (online)
  22. Combining Different In Silico Methods for Drug Design and Development: Challenges and Opportunities Sérgio F. Sousa - Virus-Host-AI Meeting (Invited Lecture) 2024/07/29 – (Figueira da Foz, Portugal)
  23. Multiscale Modelling of DNA/RNA Aptamers for Molecular Recognition Sérgio F. Sousa - XLVIII International Congress of Theoretical Chemists of Latin Expression (Chitel2025) 2025/07/17 (Cartagena-das-Indias, Colombia)
  24. Exploring the interaction between nitrosamines with PAF-AH enzyme: in silico prospection for new therapeutic strategies Isabelly Annunciato - International Conference on Integrative Bioinformatics and Computer Systems Biology (ICIBCSB - 23) - 05/10/2023 - (Milan, Italy)
  25. Understanding the mechanism of action of multi-target anti-diabetic natural compounds using Virtual Screening Carlos S. H. Shiraishi; Fábio G. Martins, Sérgio F. Sousa, Miguel A. Prieto, Sandrina A. Heleno and Rui M. V. Abreu. Academy Branch of the Conference,4th Insure Hub Conference “Innovation, Sustainability and Regeneration, October 29-30, 2024, in Porto.

Proceeding in international conferences

  1. Title:
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Posters (internation meetings)

  1. Galamba, N. Cyclic Peptides as Protein Aggregation Inhibitors for Globular and Intrinsically Disordered Disease-Related Proteins, The Leuven Protein Aggregation Meeting (2nd edition), September 11-13, 2024, Leuven, Belgium – poster
  2. Jéssica Rodrigues; Carlos Costa; Carolina Mota Natal; Ana Margarida Gonçalves Carvalho Dias; Roque, ACA; Moura Barbosa, Arménio J.. Autor correspondente: Moura Barbosa, Arménio J.. "Molecular Modeling in Biotechnology: Design and Discovery of small molecule adsorbents". Trabalho apresentado em EuroQSAR 2024, 2024.
  3. Jéssica Rodrigues; Carlos Costa; Carolina Mota Natal; Ana Margarida Dias; Roque, ACA; Moura Barbosa, Arménio J.. Autor correspondente: Moura Barbosa, Arménio J.. "In silico Affinity Ligands: Design and Discovery of small molecule adsorbents". Trabalho apresentado em Bpi Europe 2024, 2024.
  4. Moura Barbosa, Arménio J.; Soares, Cátia Lopes; Esteves, Carina; Nurrito, Ariana; Lychko, Iana; Ana Margarida Dias; Pina, Ana Sofia; Roque, Ana Cecília Afonso. "From code to structure: molecular modeling in biomaterials assembly". Trabalho apresentado em SUPRAlife Second School – “Bioinspired Supramolecular Self-Assemblies, 2024.

Posters (national meetings)

Thesis / Dissertation

PhD Thesis

Finished

Ongoing

Master Thesis

  1. Vasco Neto – MSc, “Probing the Anti-Sickling Power of Distinct Drugs in Sickle Cell Disease”, scientific advisor, Biochemistry and Biomedicine MSc, FCUL
  2. Inês Gomes – MSc, “Probing the Stability of Biomolecules in Deep Eutectic Solvents”, scientific advisor, Biochemistry and Biomedicine MSc, FCUL
  3. Catarina Nascimento – MSc, “Molecular Mechanisms of Amyloid Aggregation in Neurodegenerative Diseases”, scientific advisor, Biochemistry and Biomedicine MSc, FCUL
  4. 11/2024, Computational Modeling of Biopharmaceuticals Purification Systems, Jéssica Rodrigues, Master in Computational Biology and Bioinformatics, FCT UNL.

Finished

Ongoing

Patents

Datasets

Courses

  1. Course for Biochemistry BSc Degree: Introduction to Biomolecular Simulation, at FCT UNL. The course aims to introduce students to the field of biomolecular simulation. HPC computing time for students.
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