Innovative Therapies

Data-Driven Molecular Design

Bioinformatics

Computational Biology

Data Science

Machine Learning

Structural Modeling

Overview

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.

Former members

Publications

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Information about journal articles, updated at 03-11-2024, 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

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