Innovative Therapies
Data-Driven Molecular Design
Bioinformatics
Computational Biology
Data Science
Machine Learning
Structural Modeling
Bioinformatics
Computational Biology
Data Science
Machine Learning
Structural Modeling
Our Research Group achieved significant milestones in three key areas:
1. Enhancement Of Scientific Outcomes And Human Resources. We have substantially bolstered our scientific contributions in the last five years, securing 11 awards and authoring 30 scientific publications, including 8 with an Impact Factor (IF) > 8, alongside 11 book chapters. Remarkably, 23% in the top 10% of journals based on the JIF. The integration of data science and AI into chemistry and biomedicine is the cornerstone of our research. By developing new methodologies in these areas, we have contributed to the enhancement of predictive models, drug discovery processes, and the understanding of disease mechanisms. These advancements are not just theoretical but also have practical implications for improving the efficacy, safety, and development speed of new therapeutic solutions. In the last few years, several publications have demonstrated relevant new tools/pipelines (for example, DrugTax, DELFOS, SYNPRED, SicknessMiner, and the SARS-CoV-2 Membrane Protein Pipeline) with many others in the submission phase. We have successfully led and participated in 14 grants, directly attracting 1 million euros and more than 34 million CPU hours, in competitive funding for personnel hiring and contributing indirectly to €7 million through various projects. Our team has grown, attracting talented researchers, including two National Researcher positions, and nine PhD fellowships. We established a broad network of collaborations, both domestically and internationally, encompassing both theoretical and practical research areas. Through these targeted efforts, we make significant contributions to both biochemistry and computer science by influencing a wide range of research and development activities related to understanding health and disease, diagnostics, and therapeutics.
2. Institutional And Educational Impacts. Our group leader's roles are pivotal, serving as Vice-president of BioData.pt, Portuguese ELIXIR node coordinator for the computational biology master's program at the University of Coimbra, and BioExcel Portuguese Ambassador. We have enriched academic curricula with courses across undergraduate, master, and PhD levels and spearheaded five workshops, two conferences, and numerous national initiatives, with group members delivering over 30 presentations globally.
3. Innovation and Translation. We co-founded PURR.AI, a start-up, working on the interface of AI and neurological biosciences.
Information about journal articles, updated at 15-12-2024, from platform CIÊNCIAVITAE.
POSEIDON: Peptidic Objects SEquence-based Interaction with cellular DOmaiNs: a new database and predictor
Preto, António J.; Caniceiro, Ana B.; Duarte, Francisco; Fernandes, Hugo; Ferreira, Lino; Mourão, Joana; Moreira, Irina S., 2024. Journal of Cheminformatics. 1. 16. 2024. http://dx.doi.org/10.1186/s13321-024-00810-7 . 10.1186/s13321-024-00810-7 . Journal of Cheminformatics
pKa Calculations of GPCRs: Understanding Protonation States in Receptor Activation
Carlos A. V. Barreto; João N. M. Vitorino; Pedro B.P.S. Reis; Miguel Machuqueiro; Irina S. Moreira, 2024. Journal of Chemical Information and Modeling. 2024. https://doi.org/10.1021/acs.jcim.4c01125 . 10.1021/acs.jcim.4c01125 . Journal of Chemical Information and Modeling
Advancing Drug Safety in Drug Development: Bridging Computational Predictions for Enhanced Toxicity Prediction
Ana M. B. Amorim; Luiz F. Piochi; Ana T. Gaspar; António J. Preto; Nícia Rosário-Ferreira; Irina S. Moreira, 2024. Chemical Research in Toxicology. 2024. https://doi.org/10.1021/acs.chemrestox.3c00352 . 10.1021/acs.chemrestox.3c00352 . Chemical Research in Toxicology
Designer high-density lipoprotein particles enhance endothelial barrier function and suppress inflammation
Yueh-Chien Lin; Steven Swendeman; Irina S. Moreira; Avishek Ghosh; Andrew Kuo; Nícia Rosário-Ferreira; Shihui Guo; et al, 2024. Science Signaling. 2024. https://doi.org/10.1126/scisignal.adg9256 . 10.1126/scisignal.adg9256 . Science Signaling
DELFOS—drug efficacy leveraging forked and specialized networks—benchmarking scRNA-seq data in multi-omics-based prediction of cancer sensitivity
Luiz Felipe Piochi; António J Preto; Irina S Moreira; Jonathan Wren, 2023. Bioinformatics. 2023. https://doi.org/10.1093/bioinformatics/btad645 . 10.1093/bioinformatics/btad645 . Bioinformatics
MUG: A mutation overview of GPCR subfamily A17 receptors
Caniceiro, Ana B.; Bueschbell, Beatriz; Barreto, Carlos A.V.; Preto, António J.; Moreira, Irina S., 2023. Computational and Structural Biotechnology Journal. 586 - 600. 21. 2023. http://dx.doi.org/10.1016/j.csbj.2022.12.031 . 10.1016/j.csbj.2022.12.031 . Computational and Structural Biotechnology Journal
Network Biology and Artificial Intelligence Drive the Understanding of the Multidrug Resistance Phenotype in Cancer
2022. Drug Resistance Updates. 100811 - 100811. 2022. http://dx.doi.org/10.1016/j.drup.2022.100811 . 10.1016/j.drup.2022.100811 . Drug Resistance Updates
Class A and C GPCR dimers in neurodegenerative diseases
Caniceiro, Ana B.; Bueschbell, Beatriz; Schiedel, Anke C.; Moreira, Irina S., 2022. Current Neuropharmacology. 20. 2022. http://dx.doi.org/10.2174/1570159x20666220327221830 . 10.2174/1570159x20666220327221830 . Current Neuropharmacology
SYNPRED: prediction of drug combination effects in cancer using different synergy metrics and ensemble learning
António J Preto; Pedro Matos-Filipe; Joana Mourão; Irina S Moreira, 2022. GigaScience. 2022. https://doi.org/10.1093/gigascience/giac087 . 10.1093/gigascience/giac087 . GigaScience
DrugTax: package for drug taxonomy identification and explainable feature extraction
Preto, A. J.; Correia, Paulo C.; Moreira, Irina S., 2022. Journal of Cheminformatics. 1. 14. 2022. http://dx.doi.org/10.1186/s13321-022-00649-w . 10.1186/s13321-022-00649-w . Journal of Cheminformatics
Aberrant hippocampal transmission and behavior in mice with a stargazin mutation linked to intellectual disability
Caldeira, G. L.; Inácio, A. S.; Beltrão, N.; Barreto, C. A. V.; Rodrigues, M. V.; Rondão, T.; Macedo, R.; et al, 2022. Molecular Psychiatry. 2022. http://dx.doi.org/10.1038/s41380-022-01487-w . 10.1038/s41380-022-01487-w . Molecular Psychiatry
Using machine-learning-driven approaches to boost hot-spot's knowledge
Nícia Rosário-Ferreira; Alexandre M. J. J. Bonvin; Irina S. Moreira, 2022. WIREs Computational Molecular Science. 2022. https://doi.org/10.1002/wcms.1602 . 10.1002/wcms.1602 . WIREs Computational Molecular Science
SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights
Catarina Marques-Pereira; Manuel N. Pires; Raquel P. Gouveia; Nádia N. Pereira; Ana B. Caniceiro; Nícia Rosário-Ferreira; Irina S. Moreira, 2022. International Journal of Molecular Sciences. 2986 - 2986. 6. 23. 2022. https://doi.org/10.3390/ijms23062986 . 10.3390/ijms23062986 . International Journal of Molecular Sciences
Enhanced neuronal differentiation by dynamic piezoelectric stimulation
Pinho, Tiffany S.; Silva, Deolinda; Ribeiro, Jorge Cibrão; Marote, Ana; Lima, Rui; Batista, Salete J.; Melo, Rita; et al, 2022. Journal of Biomedical Materials Research Part A. 2022. http://dx.doi.org/10.1002/jbm.a.37443 . 10.1002/jbm.a.37443 . Journal of Biomedical Materials Research Part A
SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations
Rosário-Ferreira, Nícia; Guimarães, Victor; Costa, Vítor S.; Moreira, Irina S., 2021. BMC Bioinformatics. 1. 22. 2021. http://dx.doi.org/10.1186/s12859-021-04397-w . 10.1186/s12859-021-04397-w . BMC Bioinformatics
MENSAdb: a thorough structural analysis of membrane protein dimers
Pedro Matos-Filipe; António J Preto; Panagiotis I Koukos; Joana Mourão; Alexandre M J J Bonvin; Irina S Moreira, 2021. Database. 2021. https://doi.org/10.1093/database/baab013 . 10.1093/database/baab013 . Database
Integrated in Silico and Experimental Approach towards the Design of a Novel Recombinant Protein Containing an Anti-HER2 scFv
Joana Santos; Miguel Cardoso; Irina S. Moreira; João Gonçalves; João D. G. Correia; Sandra Cabo Verde; Rita Melo, 2021. International Journal of Molecular Sciences. 3547 - 3547. 7. 22. 2021. https://doi.org/10.3390/ijms22073547 . 10.3390/ijms22073547 . International Journal of Molecular Sciences
Decoding Partner Specificity of Opioid Receptor Family
Barreto, Carlos A. V.; Baptista, Salete J.; Preto, António J.; Silvério, Daniel; Melo, Rita; Moreira, Irina S., 2021. Frontiers in Molecular Biosciences. 8. 2021. http://dx.doi.org/10.3389/fmolb.2021.715215 . 10.3389/fmolb.2021.715215 . Frontiers in Molecular Biosciences
In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2
Rosário-Ferreira, Nícia; Baptista, Salete J.; Barreto, Carlos A. V.; Rodrigues, Filipe E. P.; Silva, Tomás F. D.; Ferreira, Sara G. F.; Vitorino, João N. M.; et al, 2021. ACS Synthetic Biology. 3209 - 3235. 11. 10. 2021. http://dx.doi.org/10.1021/acssynbio.1c00368 . 10.1021/acssynbio.1c00368 . ACS Synthetic Biology
The Treasury Chest of Text Mining: Piling Available Resources for Powerful Biomedical Text Mining
Nícia Rosário-Ferreira; Catarina Marques-Pereira; Manuel Pires; Daniel Ramalhão; Nádia Pereira; Victor Guimarães; Vítor Santos Costa; Irina Sousa Moreira, 2021. BioChem. 60 - 80. 2. 1. 2021. https://doi.org/10.3390/biochem1020007 . 10.3390/biochem1020007 . BioChem
Understanding the binding specificity of G-protein coupled receptors towards G-proteins and Arrestins: application to the dopamine receptor family
Preto, António José; Barreto, Carlos A.V.; Baptista, Salete; Almeida, Jose; Lemos, Agostinho; Melo, André; Cordeiro, Maria Natália D.S.; et al, 2020. Journal of Chemical Information and Modeling. 2020. http://dx.doi.org/10.1021/acs.jcim.0c00371 . 10.1021/acs.jcim.0c00371 . Journal of Chemical Information and Modeling
Computational modeling on mitochondrial channel nanotoxicity
Michael González-Durruthy; Amal Kanta Giri; Irina Moreira; Riccardo Concu; André Melo; Juan M. Ruso; M. Natália D.S. Cordeiro, 2020. Nano Today. 100913 - 100913. 34. 2020. https://doi.org/10.1016/j.nantod.2020.100913 . 10.1016/j.nantod.2020.100913 . Nano Today
An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45
Koukos, Panagiotis I.; Roel-Touris, Jorge; Ambrosetti, Francesco; Geng, Cunliang; Schaarschmidt, Jörg; Trellet, Mikael E.; Melquiond, Adrien S. J.; et al, 2020. Proteins: Structure, Function, and Bioinformatics. 1029 - 1036. 8. 88. 2020. http://dx.doi.org/10.1002/prot.25869 . 10.1002/prot.25869 . Proteins: Structure, Function, and Bioinformatics
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features
Preto, A. J.; Moreira, Irina S., 2020. International Journal of Molecular Sciences. 19. 21. 2020. http://dx.doi.org/10.3390/ijms21197281 . 10.3390/ijms21197281 . International Journal of Molecular Sciences
The Central Role of Non-Structural Protein 1 (NS1) in Influenza Biology and Infection
Nícia Rosário-Ferreira; António J. Preto; Rita Melo; Irina S. Moreira; Rui M. M. Brito, 2020. International Journal of Molecular Sciences. 2020. https://doi.org/10.3390/ijms21041511 . 10.3390/ijms21041511 . International Journal of Molecular Sciences
A Complete Assessment of Dopamine Receptor- Ligand Interactions through Computational Methods
Beatriz Bueschbell; Carlos Barreto; António J. Preto; Anke Schiedel; Irina Moreira, 2019. Molecules. 2019. https://www.mdpi.com/1420-3049/24/7/1196 . 10.3390/molecules24071196 . Molecules
Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization
Moreira, Irina S, 2019. Biomolecules. 2019. http://dx.doi.org/10.3390/biom9110706 . 10.3390/biom9110706 . Biomolecules
In Silico Studies Targeting G-protein Coupled Receptors for Drug Research Against Parkinson's Disease.
Lemos A; Melo R; Preto AJ; Almeida JG; Moreira IS; Dias Soeiro Cordeiro MN, 2018. Current neuropharmacology. 2018. http://europepmc.org/abstract/med/29521236 . 10.2174/1570159x16666180308161642 . Current neuropharmacology
Modulation of Protein-Protein Interactions for the Development of Effective Therapeutics - From a Joint Perspective of Experiment and Computation
Moreira, Irina Sousa; Sensoy, Ozge, 2018. Current Topics in Medicinal Chemistry. 645 - 646. 8. 18. 2018. http://dx.doi.org/10.2174/156802661808180718151704 . 10.2174/156802661808180718151704 . Current Topics in Medicinal Chemistry
Prediction and Targeting of Interaction Interfaces in G-Protein Coupled Receptor Oligomers.
Schiedel AC; Kose M; Barreto C; Bueschbell B; Morra G; Sensoy O; Moreira IS, 2018. Current topics in medicinal chemistry. 2018. http://europepmc.org/abstract/med/29866008 . 10.2174/1568026618666180604082610 . Current topics in medicinal chemistry
Computational Approaches in Antibody-drug Conjugate Optimization for Targeted Cancer Therapy
Melo, Rita; Lemos, Agostinho; Preto, Antonio J.; Almeida, Jose G.; Correia, Joao D.G.; Sensoy, Ozge; Moreira, Irina S., 2018. Current Topics in Medicinal Chemistry. 1091 - 1109. 13. 18. 2018. http://dx.doi.org/10.2174/1568026618666180731165222 . 10.2174/1568026618666180731165222 . Current Topics in Medicinal Chemistry
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.
Moreira, Irina, 2017. Journal of computer-aided molecular design. 2017. http://europepmc.org/abstract/med/28831657 . 10.1007/s10822-017-0049-y . Journal of computer-aided molecular design
Membrane proteins structures: A review on computational modeling tools
Jose G. Almeida; Antonio J. Preto; Panagiotis I. Koukos; Alexandre M.J.J. Bonvin; Irina S. Moreira, 2017. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2021 - 2039. 10. 1859. 2017. https://doi.org/10.1016/j.bbamem.2017.07.008 . 10.1016/j.bbamem.2017.07.008 . Biochimica et Biophysica Acta (BBA) - Biomembranes
SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots
Irina S. Moreira; Panagiotis I. Koukos; Rita Melo; Jose G. Almeida; Antonio J. Preto; Joerg Schaarschmidt; Mikael Trellet; et al, 2017. Scientific Reports. 2017. 10.1038/s41598-017-08321-2 . Scientific Reports
General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides.
Moreira, Irina, 2016. The journal of physical chemistry. A. 2016. http://europepmc.org/abstract/med/27267296 . 10.1021/acs.jpca.6b02250 . The journal of physical chemistry. A
A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.
Moreira, Irina, 2016. International journal of molecular sciences. 2016. http://europepmc.org/abstract/med/27472327 . 10.3390/ijms17081215 . International journal of molecular sciences
Understanding the Differential Selectivity of Arrestins toward the Phosphorylation State of the Receptor.
Moreira, Irina, 2016. ACS chemical neuroscience. 2016. http://europepmc.org/abstract/med/27405242 . 10.1021/acschemneuro.6b00073 . ACS chemical neuroscience
A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy
Moreira, Irina S.; Martins, Joao M.; Coimbra, Joa T. S.; Ramos, Maria J.; Fernandes, Pedro A., 2015. Physical Chemistry Chemical Physics. 2378 - 2387. 4. 17. 2015. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000346906700012&KeyUID=WOS:000346906700012 . 10.1039/c4cp04688a . Physical Chemistry Chemical Physics
Re(I) and Tc(I) Complexes for Targeting Nitric Oxide Synthase: Influence of the Chelator in the Affinity for the Enzyme
Oliveira, Bruno L.; Morais, Mauricio; Mendes, Filipa; Moreira, Irina S.; Cordeiro, Carlos; Fernandes, Pedro A.; Ramos, Maria J.; et al, 2015. Chemical Biology & Drug Design. 1072 - 1086. 5. 86. 2015. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000365404100013&KeyUID=WOS:000365404100013 . 10.1111/cbdd.12575 . Chemical Biology & Drug Design
The Role of Water Occlusion for the Definition of a Protein Binding Hot-Spot.
Moreira IS, 2015. Current topics in medicinal chemistry. 2015. http://europepmc.org/abstract/med/25986686 . 10.2174/1568026615666150519103733 . Current topics in medicinal chemistry
Solvent Accessible Surface Area-Based Hot-Spot Detection Methods for Protein-Protein and Protein-Nucleic Acid Interfaces
Munteanu, Cristian R.; Pimenta, Antonio C.; Fernandez-Lozano, Carlos; Melo, Andre; Cordeiro, Maria N. D. S.; Moreira, Irina S., 2015. Journal of Chemical Information and Modeling. 1077 - 1086. 5. 55. 2015. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000355382200015&KeyUID=WOS:000355382200015 . 10.1021/ci500760m . Journal of Chemical Information and Modeling
Structural features of the G-protein/GPCR interactions
Moreira, Irina S., 2014. Biochimica Et Biophysica Acta-General Subjects. 16 - 33. 1. 1840. 2014. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000330556200003&KeyUID=WOS:000330556200003 . 10.1016/j.bbagen.2013.08.027 . Biochimica Et Biophysica Acta-General Subjects
Are hot-spots occluded from water?
Moreira, Irina Sousa; Ramos, Rui Miguel; Martins, Joao Miguel; Fernandes, Pedro Alexandrino; Ramos, Maria Joao, 2014. Journal of Biomolecular Structure & Dynamics. 186 - 197. 2. 32. 2014. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000327236900002&KeyUID=WOS:000327236900002 . 10.1080/07391102.2012.758598 . Journal of Biomolecular Structure & Dynamics
Evolution of drug resistance: insight on TEM ß-lactamases structure and activity and ß-lactam antibiotics
Pimenta, A. C.; Fernandes, R.; Moreira, I. S., 2014. Mini Rev Med Chem. 111 - 22. 2. 14. 2014. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340832600002&KeyUID=WOS:000340832600002 . 10.2174/1389557514666140123145809 . Mini Rev Med Chem
Solvent-accessible surface area: How well can be applied to hot-spot detection?
Martins, Joao M.; Ramos, Rui M.; Pimenta, Antonio C.; Moreira, Irina S., 2014. Proteins-Structure Function and Bioinformatics. 479 - 490. 3. 82. 2014. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000331368200013&KeyUID=WOS:000331368200013 . 10.1002/prot.24413 . Proteins-Structure Function and Bioinformatics
Dynamic Structure of NGF and proNGF Complexed with p75NTR: Pro-Peptide Effect
Pimenta, A. C.; Dourado, D. F. A. R.; Martins, J. M.; Melo, A.; Dias Soeiro Cordeiro, M. N.; Almeida, R. D.; Morra, G.; Moreira, I. S., 2014. Journal of Chemical Information and Modeling. 2051 - 2067. 7. 54. 2014. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000339647000021&KeyUID=WOS:000339647000021 . 10.1021/ci500101n . Journal of Chemical Information and Modeling
Structural Determinants of a Typical Leucine-Rich Repeat Protein
Martins, Joao M.; Ramos, Rui M.; Moreira, Irina S., 2013. Communications in Computational Physics. 238 - 255. 1. 13. 2013. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000306807400014&KeyUID=WOS:000306807400014 . 10.4208/cicp.300711.230911s . Communications in Computational Physics
Extending the applicability of the O-ring theory to protein-DNA complexes
Ramos, R. M.; Fernandes, L. F.; Moreira, I. S., 2013. Computational Biology and Chemistry. 31 - 39. 44. 2013. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000318390200005&KeyUID=WOS:000318390200005 . 10.1016/j.compbiolchem.2013.02.005 . Computational Biology and Chemistry
Understanding the importance of the aromatic amino-acid residues as hot-spots
Moreira, I. S.; Martins, J. M.; Ramos, R. M.; Fernandes, P. A.; Ramos, M. J., 2013. Biochimica Et Biophysica Acta-Proteins and Proteomics. 404 - 414. 1. 1834. 2013. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000314620400042&KeyUID=WOS:000314620400042 . 10.1016/j.bbapap.2012.07.005 . Biochimica Et Biophysica Acta-Proteins and Proteomics
Computational Alanine Scanning Mutagenesis—An Improved Methodological Approach for Protein–DNA Complexes
Ramos, Rui M.; Moreira, Irina S., 2013. Journal of Chemical Theory and Computation. 4243 - 4256. 9. 9. 2013. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000330096800039&KeyUID=WOS:000330096800039 . 10.1021/ct400387r . Journal of Chemical Theory and Computation
Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI
Martins, Silvia A.; Perez, Marta A. S.; Moreira, Irina S.; Sousa, Sergio F.; Ramos, M. J.; Fernandes, P. A., 2013. Journal of Chemical Theory and Computation. 1311 - 1319. 3. 9. 2013. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000316168700002&KeyUID=WOS:000316168700002 . 10.1021/ct4000372 . Journal of Chemical Theory and Computation
Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms
Oliveira, B. L.; Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.; Santos, I.; Correia, J. D. G., 2013. Journal of Molecular Modeling. 1537 - 1551. 4. 19. 2013. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000316677600007&KeyUID=WOS:000316677600007 . 10.1007/s00894-012-1677-8 . Journal of Molecular Modeling
Theoretical studies on the binding of rhenium(I) complexes to inducible nitric oxide synthase
Oliveira, Bruno L.; Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.; Santos, Isabel; Correia, Joao D. G., 2013. Journal of Molecular Graphics & Modelling. 13 - 25. 45. 2013. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000326849200002&KeyUID=WOS:000326849200002 . 10.1016/j.jmgm.2013.07.007 . Journal of Molecular Graphics & Modelling
Ligand-Induced Structural Changes in TEM-1 Probed by Molecular Dynamics and Relative Binding Free Energy Calculations
Pimenta, A. C.; Martins, J. M.; Fernandes, R.; Moreira, I. S., 2013. Journal of Chemical Information and Modeling. 2648 - 2658. 10. 53. 2013. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000326480000014&KeyUID=WOS:000326480000014 . 10.1021/ci400269d . Journal of Chemical Information and Modeling
The Evolutionary Portrait of Metazoan NAD Salvage
Carneiro, J.; Duarte-Pereira, S.; Azevedo, L.; Castro, L. F. C.; Aguiar, P.; Moreira, I. S.; Amorim, A.; Silva, R. M., 2013. Plos One. 5. 8. 2013. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000319733000079&KeyUID=WOS:000319733000079 . 10.1371/journal.pone.0064674 . Plos One
CompASM: an Amber-VMD alanine scanning mutagenesis plug-in
Ribeiro, Joao V.; Cerqueira, Nuno M. F. S. A.; Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria Joao, 2012. Theoretical Chemistry Accounts. 10. 131. 2012. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000309862600005&KeyUID=WOS:000309862600005 . 10.1007/s00214-012-1271-2 . Theoretical Chemistry Accounts
Design and Characterization of Small Molecule Inhibitors of the PICK1 PDZ Domain with Binding Free Energy Calculations
Moreira, Irina; Ge, Xiaoxia; Madsen, Kenneth L.; Gether, Ulrik; Weinstein, Harel, 2010. Biophysical Journal. 428a - 428a. 3, Supplem. 98. 2010. http://dx.doi.org/10.1016/j.bpj.2009.12.2319 . Biophysical Journal
Protein-Protein Docking Dealing With the Unknown
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 2010. Journal of Computational Chemistry. 317 - 342. 2. 31. 2010. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000273412900008&KeyUID=WOS:000273412900008 . 10.1002/jcc.21276 . Journal of Computational Chemistry
Structure-activity relationships of a small-molecule inhibitor of the PDZ domain of PICK1
Bach, Anders; Stuhr-Hansen, Nicolai; Thorsen, Thor S.; Bork, Nicolai; Moreira, Irina S.; Frydenvang, Karla; Padrah, Shahrokh; et al, 2010. Organic & Biomolecular Chemistry. 4281 - 4288. 19. 8. 2010. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000282474300015&KeyUID=WOS:000282474300015 . 10.1039/c0ob00025f . Organic & Biomolecular Chemistry
Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD
Thorsen, Thor S.; Madsen, Kenneth L.; Rebola, Nelson; Rathje, Mette; Anggono, Victor; Bach, Anders; Moreira, Irina S.; et al, 2010. Proceedings of the National Academy of Sciences of the United States of America. 413 - 418. 1. 107. 2010. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000273559200072&KeyUID=WOS:000273559200072 . 10.1073/pnas.0902225107 . Proceedings of the National Academy of Sciences of the United States of America
Allosteric communication between protomers of dopamine class A GPCR dimers modulates activation
Han, Yang; Moreira, Irina S.; Urizar, Eneko; Weinstein, Harel; Javitch, Jonathan A., 2009. Nature Chemical Biology. 688 - 695. 9. 5. 2009. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000269093000018&KeyUID=WOS:000269093000018 . 10.1038/nchembio.199 . Nature Chemical Biology
Protein-protein recognition: a computational mutagenesis study of the MDM2-P53 complex
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 2008. Theoretical Chemistry Accounts. 533 - 542. 4-6. 120. 2008. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000256765900024&KeyUID=WOS:000256765900024 . 10.1007/s00214-008-0432-9 . Theoretical Chemistry Accounts
Hot spot occlusion from bulk water: A comprehensive study of the complex between the lysozyme HEL and the antibody FVD1.3
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 2007. Journal of Physical Chemistry B. 2697 - 2706. 10. 111. 2007. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000244735300037&KeyUID=WOS:000244735300037 . 10.1021/jp067096p . Journal of Physical Chemistry B
Backbone importance for protein-protein binding
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 2007. Journal of Chemical Theory and Computation. 885 - 893. 3. 3. 2007. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000246282600026&KeyUID=WOS:000246282600026 . 10.1021/ct6003824 . Journal of Chemical Theory and Computation
Computational alanine scanning mutagenesis - An improved methodological approach
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 2007. Journal of Computational Chemistry. 644 - 654. 3. 28. 2007. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000243762800003&KeyUID=WOS:000243762800003 . 10.1002/jcc.20566 . Journal of Computational Chemistry
Unravelling Hot Spots: a comprehensive computational mutagenesis study
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 2007. Theoretical Chemistry Accounts. 99 - 113. 1. 117. 2007. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000243262300010&KeyUID=WOS:000243262300010 . 10.1007/s00214-006-0151-z . Theoretical Chemistry Accounts
Hot spots-A review of the protein-protein interface determinant amino-acid residues
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 2007. Proteins-Structure Function and Bioinformatics. 803 - 812. 4. 68. 2007. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000249188900001&KeyUID=WOS:000249188900001 . 10.1002/prot.21396 . Proteins-Structure Function and Bioinformatics
Vascular endothelial growth factor (VEGF) inhibition - A critical review
Moreira, Irina Sousa; Fernandes, Pedro Alexandrino; Ramos, Maria Joao, 2007. Anti-Cancer Agents in Medicinal Chemistry. 223 - 245. 2. 7. 2007. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000244009200005&KeyUID=WOS:000244009200005 . Anti-Cancer Agents in Medicinal Chemistry
Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL-10
Moreira, I. S.; Fernandes, P. A.; Ramos, M. J., 2007. International Journal of Quantum Chemistry. 299 - 310. 2. 107. 2007. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000242652700006&KeyUID=WOS:000242652700006 . 10.1002/qua.21193 . International Journal of Quantum Chemistry
Detailed microscopic study of the full ZipA : FtsZ interface
Moreira, IS; Fernandes, PA; Ramos, MJ, 2006. Proteins-Structure Function and Bioinformatics. 811 - 821. 4. 63. 2006. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000237863100010&KeyUID=WOS:000237863100010 . 10.1002/prot.20944 . Proteins-Structure Function and Bioinformatics
Unraveling the importance of protein-protein interaction: Application of a computational alanine-scanning mutagenesis to the study of the IgG1 streptococcal protein G (C2 fragment) complex
Moreira, IS; Fernandes, PA; Ramos, MJ, 2006. Journal of Physical Chemistry B. 10962 - 10969. 22. 110. 2006. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000237954000049&KeyUID=WOS:000237954000049 . 10.1021/jp054760d . Journal of Physical Chemistry B
Accuracy of the numerical solution of the Poisson-Boltzmann equation
Moreira, IS; Fernandes, PA; Ramos, MJ, 2005. Journal of Molecular Structure-Theochem. 11 - 18. 1-2. 729. 2005. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000232258200003&KeyUID=WOS:000232258200003 . 10.1016/j.theochem.2004.12.049 . Journal of Molecular Structure-Theochem
New designs for MRI contrast agents
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, 2003. Journal of Computer-Aided Molecular Design. 463 - 473. 7. 17. 2003. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000186335800004&KeyUID=WOS:000186335800004 . 10.1023/A:1027347527385 . Journal of Computer-Aided Molecular Design
5 73 out of 73 Publications
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