Publications
Information about journal articles, updated at 17-11-2024, from platform CIÊNCIAVITAE.
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, 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
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., 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
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, 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, 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, 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., 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
Using machine-learning-driven approaches to boost hot-spot's knowledge
Nícia Rosário-Ferreira; Alexandre M. J. J. Bonvin; Irina S. Moreira, WIREs Computational Molecular Science. 2022. https://doi.org/10.1002/wcms.1602 . 10.1002/wcms.1602 . WIREs Computational Molecular Science
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, Molecular Psychiatry. 2022. http://dx.doi.org/10.1038/s41380-022-01487-w . 10.1038/s41380-022-01487-w . Molecular Psychiatry
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, International Journal of Molecular Sciences. 2986 - 2986. 6. 23. 2022. https://doi.org/10.3390/ijms23062986 . 10.3390/ijms23062986 . International Journal of Molecular Sciences
Class A and C GPCR dimers in neurodegenerative diseases
Caniceiro, Ana B.; Bueschbell, Beatriz; Schiedel, Anke C.; Moreira, Irina S., Current Neuropharmacology. 20. 2022. http://dx.doi.org/10.2174/1570159x20666220327221830 . 10.2174/1570159x20666220327221830 . Current Neuropharmacology
Network Biology and Artificial Intelligence Drive the Understanding of the Multidrug Resistance Phenotype in Cancer
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
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, 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
DrugTax: package for drug taxonomy identification and explainable feature extraction
Preto, A. J.; Correia, Paulo C.; Moreira, Irina S., 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
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, GigaScience. 2022. https://doi.org/10.1093/gigascience/giac087 . 10.1093/gigascience/giac087 . GigaScience
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, Database. 2021. https://doi.org/10.1093/database/baab013 . 10.1093/database/baab013 . Database
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, BioChem. 60 - 80. 2. 1. 2021. https://doi.org/10.3390/biochem1020007 . 10.3390/biochem1020007 . BioChem
SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations
Rosário-Ferreira, Nícia; Guimarães, Victor; Costa, Vítor S.; Moreira, Irina S., BMC Bioinformatics. 1. 22. 2021. http://dx.doi.org/10.1186/s12859-021-04397-w . 10.1186/s12859-021-04397-w . BMC Bioinformatics
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, International Journal of Molecular Sciences. 3547 - 3547. 7. 22. 2021. https://doi.org/10.3390/ijms22073547 . 10.3390/ijms22073547 . International Journal of Molecular Sciences
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, ACS Synthetic Biology. 3209 - 3235. 11. 10. 2021. http://dx.doi.org/10.1021/acssynbio.1c00368 . 10.1021/acssynbio.1c00368 . ACS Synthetic Biology
Decoding Partner Specificity of Opioid Receptor Family
Barreto, Carlos A. V.; Baptista, Salete J.; Preto, António J.; Silvério, Daniel; Melo, Rita; Moreira, Irina S., Frontiers in Molecular Biosciences. 8. 2021. http://dx.doi.org/10.3389/fmolb.2021.715215 . 10.3389/fmolb.2021.715215 . Frontiers in Molecular Biosciences
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, 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., International Journal of Molecular Sciences. 19. 21. 2020. http://dx.doi.org/10.3390/ijms21197281 . 10.3390/ijms21197281 . International Journal of Molecular Sciences
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, 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, Nano Today. 100913 - 100913. 34. 2020. https://doi.org/10.1016/j.nantod.2020.100913 . 10.1016/j.nantod.2020.100913 . Nano Today
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, International Journal of Molecular Sciences. 2020. https://doi.org/10.3390/ijms21041511 . 10.3390/ijms21041511 . International Journal of Molecular Sciences
Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization
Moreira, Irina S, Biomolecules. 2019. http://dx.doi.org/10.3390/biom9110706 . 10.3390/biom9110706 . Biomolecules
A Complete Assessment of Dopamine Receptor- Ligand Interactions through Computational Methods
Beatriz Bueschbell; Carlos Barreto; António J. Preto; Anke Schiedel; Irina Moreira, Molecules. 2019. https://www.mdpi.com/1420-3049/24/7/1196 . 10.3390/molecules24071196 . Molecules
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, 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, 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, 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., 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
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, Scientific Reports. 2017. 10.1038/s41598-017-08321-2 . Scientific Reports
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, 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
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.
Moreira, Irina, 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
Understanding the Differential Selectivity of Arrestins toward the Phosphorylation State of the Receptor.
Moreira, Irina, ACS chemical neuroscience. 2016. http://europepmc.org/abstract/med/27405242 . 10.1021/acschemneuro.6b00073 . ACS chemical neuroscience
A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.
Moreira, Irina, International journal of molecular sciences. 2016. http://europepmc.org/abstract/med/27472327 . 10.3390/ijms17081215 . International journal of molecular sciences
General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides.
Moreira, Irina, 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 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., 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
The Role of Water Occlusion for the Definition of a Protein Binding Hot-Spot.
Moreira IS, 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., 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
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, 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
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., 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
Are hot-spots occluded from water?
Moreira, Irina Sousa; Ramos, Rui Miguel; Martins, Joao Miguel; Fernandes, Pedro Alexandrino; Ramos, Maria Joao, 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., 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
Structural features of the G-protein/GPCR interactions
Moreira, Irina S., 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
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., 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
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., 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
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., 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
Computational Alanine Scanning Mutagenesis—An Improved Methodological Approach for Protein–DNA Complexes
Ramos, Rui M.; Moreira, Irina S., 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
Extending the applicability of the O-ring theory to protein-DNA complexes
Ramos, R. M.; Fernandes, L. F.; Moreira, I. S., 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
Structural Determinants of a Typical Leucine-Rich Repeat Protein
Martins, Joao M.; Ramos, Rui M.; Moreira, Irina S., 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
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., 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
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., 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., 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
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., 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
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, 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
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, 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
Protein-Protein Docking Dealing With the Unknown
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 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
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, Biophysical Journal. 428a - 428a. 3, Supplem. 98. 2010. http://dx.doi.org/10.1016/j.bpj.2009.12.2319 . Biophysical Journal
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, 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
Allosteric communication between protomers of dopamine class A GPCR dimers modulates activation
Han, Yang; Moreira, Irina S.; Urizar, Eneko; Weinstein, Harel; Javitch, Jonathan A., 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., 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
Unravelling Hot Spots: a comprehensive computational mutagenesis study
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 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 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., 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
Backbone importance for protein-protein binding
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 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., 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
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., 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
Hot spots-A review of the protein-protein interface determinant amino-acid residues
Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J., 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, 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
Detailed microscopic study of the full ZipA : FtsZ interface
Moreira, IS; Fernandes, PA; Ramos, MJ, 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, 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, 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, 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
All projects
Information of exclusive responsibility of the researcher 17-11-2024 , from platform CIÊNCIAVITAE.
2022 -
Coupling CpHMD with MMPBSA to Study the Dopaminergic GPCRs Binding Interaction
2022.11124.BD
Supervisor
Funders: Fundação para a Ciência e a Tecnologia
2022 -
Pluridimensional signaling of GPCR - understanding mutagenesis effect on the receptorsome
2022.12479.BD
Supervisor
2022 -
Combining network biology and artificial intelligence to improve cancer drugs synergy predictions
2022.12975.BD
Supervisor
Universidade de Coimbra
Funders: Fundação para a Ciência e a Tecnologia
2022 -
The structural insight into the ACE2 receptor and its role in the SARS-CoV-2 infection
2022.15349.BD
Supervisor
Funders: Fundação para a Ciência e a Tecnologia
2022 - 2022
EuroCC Portugal - National Competence Centres in the framework of EuroHPC
951732 – EUROCC – H2020-JTI-EuroHPC-2019-2
Researcher
Universidade de Coimbra
Funders: EU Framework Programme for Research and Innovation Euratom
2022/12 - 2023/12
Molecular-level understanding of receptor binding of engineered high-density lipoprotein particles that chaperone bioactive lipid mediator sphingosine 1-phosphate
MCB220005P
Co-Principal Investigator (Co-PI)
Funders: National Academies of Sciences Engineering and Medicine
2021/01/01 - 2025/12/31
Center for Innovative Biomedicine and Biotechnology - Associate Laboratory
LA/P/0058/2020
Universidade de Coimbra
Funders: Fundação para a Ciência e a Tecnologia
2021/09 - 2025
The Interaction between Stargazin and Kv7.2 and its Association with Psychiatric Disorders
2021.08282.BD
Supervisor
Universidade de Coimbra
Funders: Fundação para a Ciência e a Tecnologia
2020 - 2024
Dynamic brain function: towards the understanding and treatment of brain disorders
H2020-WIDESPE-2018-2020-6
Researcher
Universidade de Coimbra Centro de Neurociências e Biologia Celular
Funders: European Commission
2020 -
Characterization of protein-protein interactions involving G-Protein-Coupled Receptor 143 by computational and pharmacological methods
SFRH/BD/149709/2019
Supervisor
Funders: Fundação para a Ciência e a Tecnologia
2020/09 -
Cutting-Edge Virus-Host Interactome Discovery
2020.07766.BD
Supervisor
Funders: Fundação para a Ciência e a Tecnologia
2020/11 - 2023
Potassium channel dysfunction in models of neurodevelopmental disorders
HR20-00904
Researcher
Universidade de Coimbra Centro de Neurociências e Biologia Celular
Funders: Caixabank SA; Fundação para a Ciência e a Tecnologia
2020 -
Cutting-Edge Virus-Host Interactome Discovery: A Multi-Omics AI Driven Approach
DSAIPA/DS/0118/2020
Principal investigator
Universidade de Coimbra Centro de Neurociências e Biologia Celular
Funders: Fundação para a Ciência e a Tecnologia
2020/12 - 2021/09
Structural and functional role of CACNG2 gene mutations in psychiatric diseases
CPCA/A0/7302/2020
Principal investigator
Funders: Fundação para a Ciência e a Tecnologia
2020/12 - 2021/12
Dissecting dopamine receptor 2 functional mechanism
CPCA/A2/7219/2020
Principal investigator
Funders: Fundação para a Ciência e a Tecnologia
2019 -
A computational approach to the structural and dynamical characterization of the ghrelin receptor function and mechanism
SFRH/BD/145457/2019
Supervisor
Funders: Fundação para a Ciência e a Tecnologia
2019 -
CIBB Statergic Plan
UIDB/04539/2020
Researcher
Fundação para a Ciência e a Tecnologia
Funders: Fundação para a Ciência e a Tecnologia
2019 - 2022
ERNEST – European research Network on Signal Transduction
CA18133
Researcher
European Cooperation in Science and Technology
Funders: European Cooperation in Science and Technology
2019 - 2022
ADHEsion GPCR Network: Research and Implementation Set the path for future Exploration
CA18240
Researcher
Funders: European Cooperation in Science and Technology
2019/01/01 - 2019/12/31
CNC. IBILI
UID/NEU/04539/2019
Universidade de Coimbra Centro de Neurociências e Biologia Celular; Universidade de Coimbra; Universidade de Coimbra Instituto de Ciências Nucleares Aplicadas à Saúde; Universidade de Coimbra Instituto de Investigação Clínica e Biomédica de Coimbra
Funders: Fundação para a Ciência e a Tecnologia
2019 - 2022
Deep-Learning application to in silico Drug Design
SFRH/BD/144966/2019
Supervisor
Universidade de Coimbra
Funders: Fundação para a Ciência e a Tecnologia
2018/04/01 - 2019
Conformational dynamics, assembly and inhibition of GPCR oligomers
2017174234
Researcher
Funders: Partnership for Advanced Computing In Europe
2018 - 2022
STRATAGEM - New diagnostic and therapeutic tools against multidrug resistant tumours
CA17104
Researcher
Funders: European Cooperation in Science and Technology
2018/09 - 2021/08
Targeting the transporters of cationic amino acids for cancer theranostics: experimental and computational chemistry approach
PTDC/QUI-NUC/30147/2017
Researcher
Funders: Fundação para a Ciência e a Tecnologia
2018/09/03 - 2022/06/02
Membrane proteins - development of new computational approaches and its application to G-Protein Coupled Receptors
PTDC/QUI-OUT/32243/2017
Principal investigator
Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento; Universidade de Coimbra Centro de Neurociências e Biologia Celular
Funders: Fundação para a Ciência e a Tecnologia
2018/06 - 2021/05
Deep learning in cancer drug discovery: a pipeline for the generation of new therapies
02/SAICT/2017/031356
Universidade de Coimbra Centro de Neurociências e Biologia Celular; Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência; Weill Cornell Medicine Department of Physiology and Biophysics; Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência Center for Research in Advanced Computing Systems; Universiteit Utrecht
Funders: Fundação para a Ciência e a Tecnologia; Associação para a Inovação e Desenvolvimento da FCT
2017 - 2018
Structural and dynamic understanding of the ghrelin receptor function on memory and learning: a computational perspective
NWO16425
Researcher
Funders: Nederlandse Organisatie voor Wetenschappelijk Onderzoek
2017/01/01 - 2019
Early Detection, neuro-modelation and advanced therapies to brain disorders (institutionally-driven project)
CENTRO-01-0145-FEDER-000008: BrainHealth 2020
Researcher
CNC.IBILI
Funders: European Regional Development Fund
2016 - 2018
Marie Sklodowska-Curie Individual Fellowship MSCA-IF-2015
MEMBRANEPROT 659826
Integration into Research Grant Fellow
Universiteit Utrecht
2015/01/15 - 2019
Molecular mechanisms in signaling selectivity of G-Protein Coupled Receptors (GPCRs)
IF/00578/2014
Principal investigator
CNC.IBILI
Funders: Fundação para a Ciência e a Tecnologia
2015 - 2016
Biased agonism in the dopamine receptor
ISCRA A BiaDop HP10CIQNJW
Researcher
Funders: Cineca
2014 - 2015
In silico design of enzymatic anti-oxidant systems 2
IDEAS
Researcher
Funders: Cineca
2014 - 2018
Target-specific delivery of radioactivity to cancer cells by virus-like particles: a computational chemistry and bioengineering approach
SFRH/BPD/97650/2013
Supervisor
Funders: Fundação para a Ciência e a Tecnologia
2013 - 2014
In silico design of semi i-synthetic functional mimics of glutathione peroxidase: from the rational choice of the organochalcogen to its bioincorporation in protein scaffols
IDEAS- CINECA
Researcher
Funders: Cineca
2012/02/01 - 2015/04/30
Nitric Oxide Synthase targeting with Re(I)/99mTc(I)-complexes containing L-Arg derivatives: A structure-activity study
PTDC/QUI-QUI/121752/2010
Researcher
Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento; Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares; Associação para a Inovação e Desenvolvimento da FCT
Funders: Fundação para a Ciência e a Tecnologia
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; Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente; Rede de Química e Tecnologia Laboratório Associado para a Química Verde
Funders: Fundação para a Ciência e a Tecnologia
5 36 out of 36 projects
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