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Identification

Personal identification

Full name
Irina de Sousa Moreira

Citation names

  • Moreira, Irina S

Author identifiers

Ciência ID
E516-94C9-7B1B
ORCID iD
0000-0003-2970-5250
Google Scholar ID
https://scholar.google.com/citations?user=8D0bgIIAAAAJ&hl=en
Researcher Id
K-4711-2012
Scopus Author Id
57191249780

Email addresses

  • irina.moreira@cnc.uc.pt (Personal)
  • irina.moreira@cnc.uc.pt (Personal)

Addresses

  • UC-Biotech Parque Tecnológico de Cantanhede, Núcleo 04, Lote B, 3060-197 , Cantanhede, Coimbra, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Chemical Sciences
  • Natural sciences - Biological Sciences - Biochemistry
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Medical and Health Sciences - Medical Biotechnology - Health-Related Biotechnology
  • Engineering and Technology - Other Engineering and Technologies - Other Engineering and Technologies

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Education
Degree Classification
2020/09
Concluded
 Engenharia Matemática (Mestrado)
Universidade do Porto Departamento de Matemática, Portugal
"Supervised Classification applied to hot-spot detection in protein-protein interfaces" (THESIS/DISSERTATION)
2016 - 2018
Concluded
 Marie Curie Fellow (Pós-doutoramento)
Major in Bioinformatics and Modelling
Universiteit Utrecht, Netherlands
2008 - 2009
Concluded
 In silico characterization of GPCRs (Pós-doutoramento)
Major in Computational Biology and Biophysics
Cornell University Joan and Sanford I Weill Medical College, United States
2008/06/18
Concluded
 Química (Doutoramento)
Major in Sub-area: Computational Biochemistry
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Departamento de Química e Bioquímica, Portugal
"Design of Anti-cancer Drugs That Target the Vascular Endothelial Growth Factor (vegf)" (THESIS/DISSERTATION)
1998 - 2003
Concluded
 Bioquímica (Licenciatura)
Major in Applied Biochemistry - Engenheiro António Almeida Award for the top grade attained in Biochemistry 2003
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Departamento de Química e Bioquímica, Portugal
"Genetic Study of Spinocerebellar Ataxias and Familial Hemiplegic Migraine caused by Calcium Channel" (THESIS/DISSERTATION)
Affiliation

Science

Category
Host institution 		Employer
2015 - 2019 Auxiliary Researcher (Research) Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2016 - 2018 Postdoc (Research) Universiteit Utrecht, Netherlands
Universiteit Utrecht, Netherlands
2009 - 2014 Auxiliary Researcher (Research) Universidade do Porto Faculdade de Ciências, Portugal
2008 - 2009 Postdoc (Research) Cornell University Joan and Sanford I Weill Medical College, United States

Teaching in Higher Education

Category
Host institution 		Employer
2019 - Current Assistant Professor (University Teacher) Universidade de Coimbra, Portugal

Positions / Appointments

Category
Host institution 		Employer
2021/09 - Current Vice-President BioData.pt, Portugal

Others

Category
Host institution 		Employer
2023/08/17 - Current Co-Founder PURR.AI, Portugal
PURR.AI, Portugal
2020/09 - Current Coordinator of the Master Degree in Computational Biology Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2015 - Current Group Leader of "Data Driven Molecular Design" Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
Projects

Grant

Designation Funders
2022 - Current Coupling CpHMD with MMPBSA to Study the Dopaminergic GPCRs Binding Interaction
2022.11124.BD
Supervisor
Fundação para a Ciência e a Tecnologia
Ongoing
2021/09 - Current The Interaction between Stargazin and Kv7.2 and its Association with Psychiatric Disorders
2021.08282.BD
Supervisor
Universidade de Coimbra, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2020/09 - Current Cutting-Edge Virus-Host Interactome Discovery
2020.07766.BD
Supervisor
Fundação para a Ciência e a Tecnologia
2020 - Current 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, Portugal
 European Commission
2020 - Current 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, Portugal
 Fundação para a Ciência e a Tecnologia
2019 - Current CIBB Statergic Plan
UIDB/04539/2020
Researcher
Fundação para a Ciência e a Tecnologia, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2020 - 2024 Characterization of protein-protein interactions involving G-Protein-Coupled Receptor 143 by computational and pharmacological methods
SFRH/BD/149709/2019
Supervisor
Fundação para a Ciência e a Tecnologia
2019 - 2024 A computational approach to the structural and dynamical characterization of the ghrelin receptor function and mechanism
SFRH/BD/145457/2019
Supervisor
Fundação para a Ciência e a Tecnologia
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)
National Academies of Sciences Engineering and Medicine
Ongoing
2020/11 - 2023 Potassium channel dysfunction in models of neurodevelopmental disorders
HR20-00904
Researcher
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
 Caixabank SA

Fundação para a Ciência e a Tecnologia
Ongoing
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, Portugal

Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2022 - 2022 EuroCC Portugal - National Competence Centres in the framework of EuroHPC
951732 – EUROCC – H2020-JTI-EuroHPC-2019-2
Researcher
Universidade de Coimbra, Portugal
 EU Framework Programme for Research and Innovation Euratom
Concluded
2019 - 2022 ERNEST – European research Network on Signal Transduction
CA18133
Researcher
European Cooperation in Science and Technology, Belgium
 European Cooperation in Science and Technology
Concluded
2019 - 2022 ADHEsion GPCR Network: Research and Implementation Set the path for future Exploration
CA18240
Researcher
European Cooperation in Science and Technology
Concluded
2019 - 2022 Deep-Learning application to in silico Drug Design
SFRH/BD/144966/2019
Supervisor
Universidade de Coimbra, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2018 - 2022 STRATAGEM - New diagnostic and therapeutic tools against multidrug resistant tumours
CA17104
Researcher
European Cooperation in Science and Technology
Concluded
2020/12 - 2021/12 Dissecting dopamine receptor 2 functional mechanism
CPCA/A2/7219/2020
Principal investigator
Fundação para a Ciência e a Tecnologia
Concluded
2020/12 - 2021/09 Structural and functional role of CACNG2 gene mutations in psychiatric diseases
CPCA/A0/7302/2020
Principal investigator
Fundação para a Ciência e a Tecnologia
Concluded
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
Fundação para a Ciência e a Tecnologia
Concluded
2018/06 - 2021/05 Deep learning in cancer drug discovery: a pipeline for the generation of new therapies
02/SAICT/2017/031356
PTDC/CCI-BIO/31356/2017
POCI-01-0145-FEDER-03135
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal

Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência, Portugal

Weill Cornell Medicine Department of Physiology and Biophysics, United States

Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência Center for Research in Advanced Computing Systems, Portugal

Universiteit Utrecht, Netherlands
Fundação para a Ciência e a Tecnologia

Associação para a Inovação e Desenvolvimento da FCT
Concluded
2018/04/01 - 2019 Conformational dynamics, assembly and inhibition of GPCR oligomers
2017174234
Researcher
Partnership for Advanced Computing In Europe
Concluded
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, Portugal
 European Regional Development Fund
Concluded
2015/01/15 - 2019 Molecular mechanisms in signaling selectivity of G-Protein Coupled Receptors (GPCRs)
IF/00578/2014
Principal investigator
CNC.IBILI, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2017 - 2018 Structural and dynamic understanding of the ghrelin receptor function on memory and learning: a computational perspective
NWO16425
Researcher
Nederlandse Organisatie voor Wetenschappelijk Onderzoek
Concluded
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
Fundação para a Ciência e a Tecnologia
Concluded
2015 - 2016 Biased agonism in the dopamine receptor
ISCRA A BiaDop HP10CIQNJW
Researcher
Cineca
Concluded
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
Provided by PTCRIS: 121752
Researcher
Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal

Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2014 - 2015 In silico design of enzymatic anti-oxidant systems 2
IDEAS
Researcher
Cineca
Concluded
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
Cineca
Concluded

Contract

Designation Funders
2022 - Current The structural insight into the ACE2 receptor and its role in the SARS-CoV-2 infection
2022.15349.BD
Supervisor
Fundação para a Ciência e a Tecnologia
Ongoing
2022 - Current Combining network biology and artificial intelligence to improve cancer drugs synergy predictions
2022.12975.BD
Supervisor
Universidade de Coimbra, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2022 - Current Pluridimensional signaling of GPCR - understanding mutagenesis effect on the receptorsome
2022.12479.BD
Supervisor
2021/01/01 - 2025/12/31 Center for Innovative Biomedicine and Biotechnology - Associate Laboratory
LA/P/0058/2020
Universidade de Coimbra, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - 2019/12/31 CNC. IBILI
UID/NEU/04539/2019
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal

Universidade de Coimbra, Portugal

Universidade de Coimbra Instituto de Ciências Nucleares Aplicadas à Saúde, Portugal

Universidade de Coimbra Instituto de Investigação Clínica e Biomédica de Coimbra, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016 - 2018 Marie Sklodowska-Curie Individual Fellowship MSCA-IF-2015
MEMBRANEPROT 659826
Integration into Research Grant Fellow
Universiteit Utrecht, Netherlands
Concluded
2011/01/01 - 2012/12/31 Strategic Project - LA 6 - 2011-2012
PEst-C/EQB/LA0006/2011
Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Moreira, Irina S; Machuqueiro, Miguel; Mourão, Joana. Computational Design of Membrane Proteins. Springer {US. 2021.
    In press • 10.1007/978-1-0716-1468-6
Book chapter
  1. "Discovery of Virus-Host interactions using bioinformatic tools". Elsevier, 2022.
    10.1016/bs.mcb.2022.02.001
  2. António J. Preto; Pedro Matos-Filipe; José G. de Almeida; Joana Mourão; Irina S. Moreira; Moreira, Irina S. "Predicting Hot Spots Using a Deep Neural Network Approach". In Artificial Neural Networks, 267-288. United States: Springer {US, 2021.
    In press • 10.1007/978-1-0716-0826-5_13
  3. Rosário-Ferreira, Nicia; Marques, Ana Catarina; Gouveia, Raquel; Mourão, Joana; Moreira, Irina S. "Guardians of the cell: State-of-the-art of membrane proteins from a computational point-of-view". In Computational Design of Membrane Proteins. 2021.
    In press
  4. Preto, A.J.; Marques, Ana Catarina; Baptista, Salete J.; Bueschbell, Beatriz; Barreto, Carlos A.V.; Gaspar, AT; Pinheiro, Ian; et al. "Targeting GPCRs via Multi-platforms arrays and AI". In Comprehensive Pharmacology. Elsevier, 2021.
    In press • 10.1016/b978-0-12-820472-6.00048-7
  5. António J. Preto; Matos-Filipe, Pedro; Panagiotis I. Koukos; Pedro Renault; Sousa, Sergio F.; Moreira, Irina S. "Structural Characterization of Membrane Protein Dimers". 2019.
    10.1007/978-1-4939-9161-7_21
  6. António J. Preto; Jose G. Almeida; Joerg Schaarschmidt; Li C. Xue; Moreira, Irina S; Alexandre M.J.J. Bonvin. "Computational Tools for the Structural Characterization of Proteins and Their Complexes from Sequence-Evolutionary Data". 2018.
    10.1002/9780470027318.a9615
  7. Lemos, Agostinho; Melo, Rita; Moreira, Irina S.; Cordeiro, M. Natália D. S.. "Computer-Aided Drug Design Approaches to Study Key Therapeutic Targets in Alzheimer’s Disease". In Computational Modeling of Drugs Against Alzheimer’s Disease, 61-106. Springer New York, 2017.
    10.1007/978-1-4939-7404-7_3
  8. Sensoy, Ozge; Almeida, Jose G.; Shabbir, Javeria; Moreira, Irina S.; Morra, Giulia; Sensoy O; Almeida JG; et al. "Computational studies of G protein-coupled receptor complexes: Structure and dynamics". In G Protein-Coupled Receptors Part A, 205-245. Elsevier, 2017.
    10.1016/bs.mcb.2017.07.011
  9. Moreira, Irina S.; Shi, Lei; Freyberg, Zachary; Ericksen, Spencer S.; Weinstein, Harel; Javitch, Jonathan A.. "Structural Basis of Dopamine Receptor Activation". In The Dopamine Receptors, 47-73. Humana Press, 2009.
    10.1007/978-1-60327-333-6_3
  10. Moreira, IrinaS; Fernandes, PedroA; Ramos, MariaJ. "Computational Determination of the Relative Free Energy of Binding – Application to Alanine Scanning Mutagenesis". edited by Sokalski, W. Andrzej, 305-339. 2007.
    10.1007/1-4020-5372-X_6
Conference poster
  1. Caldeira, Gladys Lima; Inácio, Ângela S.; Beltrão, Nuno; Barreto, Carlos A.V.; Ventura Rodrigues, Marina; Rondão, Tiago; Macedo, Renato; et al. "Aberrant hippocampal transmission and behavior in mice with stargazin mutation linked to intellectual disability.". Paper presented in SPN2021, 2022.
  2. Ventura Rodrigues, Marina; Inácio, Ângela S.; Caldeira, Gladys Lima; Gouveia, Raquel P; Barreto, Carlos A.V.; Beltrão, Nuno; Moreira, Irina S; Taglialatela, Maurizio; Carvalho, Ana Luisa. "Stargazin as a Regulator of Neuronal Excitability". Paper presented in SPN2021, 2022.
  3. Novo, João Pedro; Caetano, Carolina; L. Gee; Moreira, Irina S; Diana Jurk; Rosa, Susana; Ferreira, Lino. "The transition from a young to aged BBB is mediated in part by a senescence brain endothelial cell program". Paper presented in 1st MIA Portugal Spring School on Aging, 2022.
  4. João Pedro da Costa Novo; Ana Carolina Silva Caetano; Lucy Gee; Moreira, Irina S; Diana Jurk; Rosa, Susana; Lino da Silva Ferreira. "The transition from a young to aged BBB is mediated in part by a senescence brain endothelial cell program. J.P. Novo, A.C. Caetano, L. Gee, I. Moreira, D. Jurk, S. Rosa*, L. Silva Ferreira*. *Authors with equal contribution.". Paper presented in 12th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies (SPCE TC). 10-11th March 2022. Braga, Portugal., 2022.
  5. Pinho, Tiffany S.; Silva, Deolinda; Ribeiro, Jorge Cibrão; Marote, Ana; Lima Rui; Batista, Salete J; Melo, Rita; et al. "Dynamic Piezoelectric Stimulation Promotes Neuronal Differentiation". Paper presented in 12th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, Braga, Portugal, 2022.
  6. Pinho, Tiffany; Silva, Deolinda; Ribeiro, Jorge Cibrão; Marote, Ana; Gomes, Eduardo D; Lima, Rui; Batista, Salete J; et al. "Neuronal Differentiation on Electroactive PVDF Films Dynamically Stimulated". Paper presented in XVII Meeting of the Portuguese Society for Neuroscience, 2021.
  7. Rosário-Ferreira, Nicia; Melo, Rita; Moreira, Irina S; Rui M M Brito. "NS1 dimer behavior through a Molecular Dynamics lens". Paper presented in Coimbra Chemistry Centre Day, 2021.
  8. Gouveia, Raquel; Barreto, Carlos A.V.; Baptista, Salete J.; Caldeira, Gladys Lima; Preto, A.J.; Melo, Rita; Carvalho, Ana Luisa; Moreira, Irina S. "The Structural and Functional Role of a CACNG2 Mutation in Psychiatric Disorders". Paper presented in Bioinformatics Open Days, 2021.
  9. Gouveia, Raquel; Barreto, Carlos A.V.; Baptista, Salete J.; Caldeira, Gladys Lima; A. J. Preto; Melo, Rita; Carvalho, Ana Luisa; Moreira, Irina S. "The study of AMPAR:Stargazin interface through molecular dynamics". Paper presented in Encontro Jovens Investigadores de Biologia Estrutural e Computacional, 2021.
  10. Rosário-Ferreira, Nicia; Guimarães, Victor; Costa, Vítor; Moreira, Irina S. "Boosting network biology using a cutting-edge text-mining approach". Paper presented in Network Biology, 2021.
  11. Rosário-Ferreira, Nicia; Melo, Rita; Moreira, Irina S; Rui M M Brito. "A molecular Dynamics study of non-structural protein1 (NS1)". Paper presented in Advances in Computational Biology Conference ¿ Fostering Collaboration Among Women Scientists, 2019.
  12. Rosário-Ferreira, Nicia; Melo, Rita; Moreira, Irina S; Rui M M Brito. "Understanding the role of the non-structural protein I in the pathogenicity of influenza virus using a computational approach". Paper presented in Structural Bioinformatics Course, 2019.
  13. Rosário-Ferreira, Nicia; Melo, Rita; Moreira, Irina S; Rui M M Brito. "An integrative approach to understand protein plasticity ¿ The case of non-structural protein 1 from the influenza virus". Paper presented in PTNMR Satellite Meeting, 2019.
  14. Rosário-Ferreira, Nicia; Melo, Rita; Moreira, Irina S; Rui M M Brito. "A Molecular Dynamics Insight to Non-Structural Protein 1 (NS1) ¿ A Hub Protein Essential for Influenza Infection.". Paper presented in 4th Instruct Biennial Structural Biology Conference, 2019.
  15. Rosário-Ferreira, Nicia; Melo, Rita; Moreira, Irina S; Rui M M Brito. "Outline of a Molecular Dynamics Approach to Non- Structural Protein 1 (NS1) ¿ A Hub Protein essential for Influenza Infection". Paper presented in Encontro de Jovens Investigadores de Biologia Computacional Estrutural, 2018.
Journal article
  1. Carlos A. V. Barreto; João N. M. Vitorino; Pedro B.P.S. Reis; Miguel Machuqueiro; Irina S. Moreira. "pKa Calculations of GPCRs: Understanding Protonation States in Receptor Activation". Journal of Chemical Information and Modeling (2024): https://doi.org/10.1021/acs.jcim.4c01125.
    10.1021/acs.jcim.4c01125
  2. Ana M. B. Amorim; Luiz F. Piochi; Ana T. Gaspar; António J. Preto; Nícia Rosário-Ferreira; Irina S. Moreira. "Advancing Drug Safety in Drug Development: Bridging Computational Predictions for Enhanced Toxicity Prediction". Chemical Research in Toxicology (2024): https://doi.org/10.1021/acs.chemrestox.3c00352.
    10.1021/acs.chemrestox.3c00352
  3. Yueh-Chien Lin; Steven Swendeman; Irina S. Moreira; Avishek Ghosh; Andrew Kuo; Nícia Rosário-Ferreira; Shihui Guo; et al. "Designer high-density lipoprotein particles enhance endothelial barrier function and suppress inflammation". Science Signaling (2024): https://doi.org/10.1126/scisignal.adg9256.
    10.1126/scisignal.adg9256
  4. Preto, António J.; Caniceiro, Ana B.; Duarte, Francisco; Fernandes, Hugo; Ferreira, Lino; Mourão, Joana; Moreira, Irina S.. "POSEIDON: Peptidic Objects SEquence-based Interaction with cellular DOmaiNs: a new database and predictor". Journal of Cheminformatics 16 1 (2024): http://dx.doi.org/10.1186/s13321-024-00810-7.
    10.1186/s13321-024-00810-7
  5. Luiz Felipe Piochi; António J Preto; Irina S Moreira; Jonathan Wren. "DELFOS—drug efficacy leveraging forked and specialized networks—benchmarking scRNA-seq data in multi-omics-based prediction of cancer sensitivity". Bioinformatics (2023): https://doi.org/10.1093/bioinformatics/btad645.
    10.1093/bioinformatics/btad645
  6. Caniceiro, Ana B.; Bueschbell, Beatriz; Barreto, Carlos A.V.; Preto, António J.; Moreira, Irina S.. "MUG: A mutation overview of GPCR subfamily A17 receptors". Computational and Structural Biotechnology Journal 21 (2023): 586-600. http://dx.doi.org/10.1016/j.csbj.2022.12.031.
    10.1016/j.csbj.2022.12.031
  7. Preto, A. J.; Correia, Paulo C.; Moreira, Irina S.. "DrugTax: package for drug taxonomy identification and explainable feature extraction". Journal of Cheminformatics 14 1 (2022): http://dx.doi.org/10.1186/s13321-022-00649-w.
    10.1186/s13321-022-00649-w
  8. António J Preto; Pedro Matos-Filipe; Joana Mourão; Irina S Moreira. "SYNPRED: prediction of drug combination effects in cancer using different synergy metrics and ensemble learning". GigaScience (2022): https://doi.org/10.1093/gigascience/giac087.
    10.1093/gigascience/giac087
  9. Pinho, Tiffany S.; Silva, Deolinda; Ribeiro, Jorge Cibrão; Marote, Ana; Lima, Rui; Batista, Salete J.; Melo, Rita; et al. "Enhanced neuronal differentiation by dynamic piezoelectric stimulation". Journal of Biomedical Materials Research Part A (2022): http://dx.doi.org/10.1002/jbm.a.37443.
    10.1002/jbm.a.37443
  10. Caniceiro, Ana B.; Bueschbell, Beatriz; Schiedel, Anke C.; Moreira, Irina S.. "Class A and C GPCR dimers in neurodegenerative diseases". Current Neuropharmacology 20 (2022): http://dx.doi.org/10.2174/1570159x20666220327221830.
    10.2174/1570159x20666220327221830
  11. Catarina Marques-Pereira; Manuel N. Pires; Raquel P. Gouveia; Nádia N. Pereira; Ana B. Caniceiro; Nícia Rosário-Ferreira; Irina S. Moreira. "SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights". International Journal of Molecular Sciences 23 6 (2022): 2986-2986. https://doi.org/10.3390/ijms23062986.
    10.3390/ijms23062986
  12. Caldeira, G. L.; Inácio, A. S.; Beltrão, N.; Barreto, C. A. V.; Rodrigues, M. V.; Rondão, T.; Macedo, R.; et al. "Aberrant hippocampal transmission and behavior in mice with a stargazin mutation linked to intellectual disability". Molecular Psychiatry (2022): http://dx.doi.org/10.1038/s41380-022-01487-w.
    10.1038/s41380-022-01487-w
  13. Nícia Rosário-Ferreira; Alexandre M. J. J. Bonvin; Irina S. Moreira. "Using machine-learning-driven approaches to boost hot-spot's knowledge". WIREs Computational Molecular Science (2022): https://doi.org/10.1002/wcms.1602.
    10.1002/wcms.1602
  14. "Network Biology and Artificial Intelligence Drive the Understanding of the Multidrug Resistance Phenotype in Cancer". Drug Resistance Updates (2022): 100811-100811. http://dx.doi.org/10.1016/j.drup.2022.100811.
    10.1016/j.drup.2022.100811
  15. 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. "In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2". ACS Synthetic Biology 10 11 (2021): 3209-3235. http://dx.doi.org/10.1021/acssynbio.1c00368.
    10.1021/acssynbio.1c00368
  16. Rosário-Ferreira, Nícia; Guimarães, Victor; Costa, Vítor S.; Moreira, Irina S.. "SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations". BMC Bioinformatics 22 1 (2021): http://dx.doi.org/10.1186/s12859-021-04397-w.
    10.1186/s12859-021-04397-w
  17. Barreto, Carlos A. V.; Baptista, Salete J.; Preto, António J.; Silvério, Daniel; Melo, Rita; Moreira, Irina S.. "Decoding Partner Specificity of Opioid Receptor Family". Frontiers in Molecular Biosciences 8 (2021): http://dx.doi.org/10.3389/fmolb.2021.715215.
    10.3389/fmolb.2021.715215
  18. Nícia Rosário-Ferreira; Catarina Marques-Pereira; Manuel Pires; Daniel Ramalhão; Nádia Pereira; Victor Guimarães; Vítor Santos Costa; Irina Sousa Moreira. "The Treasury Chest of Text Mining: Piling Available Resources for Powerful Biomedical Text Mining". BioChem 1 2 (2021): 60-80. https://doi.org/10.3390/biochem1020007.
    10.3390/biochem1020007
  19. Pedro Matos-Filipe; António J Preto; Panagiotis I Koukos; Joana Mourão; Alexandre M J J Bonvin; Irina S Moreira. "MENSAdb: a thorough structural analysis of membrane protein dimers". Database (2021): https://doi.org/10.1093/database/baab013.
    10.1093/database/baab013
  20. Joana Santos; Miguel Cardoso; Irina S. Moreira; João Gonçalves; João D. G. Correia; Sandra Cabo Verde; Rita Melo. "Integrated in Silico and Experimental Approach towards the Design of a Novel Recombinant Protein Containing an Anti-HER2 scFv". International Journal of Molecular Sciences 22 7 (2021): 3547-3547. https://doi.org/10.3390/ijms22073547.
    10.3390/ijms22073547
  21. Preto, A. J.; Moreira, Irina S.. "SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features". International Journal of Molecular Sciences 21 19 (2020): 7281. http://dx.doi.org/10.3390/ijms21197281.
    10.3390/ijms21197281
  22. Michael González-Durruthy; Amal Kanta Giri; Irina Moreira; Riccardo Concu; André Melo; Juan M. Ruso; M. Natália D.S. Cordeiro. "Computational modeling on mitochondrial channel nanotoxicity". Nano Today 34 (2020): 100913-100913. https://doi.org/10.1016/j.nantod.2020.100913.
    10.1016/j.nantod.2020.100913
  23. Preto, António José; Barreto, Carlos A.V.; Baptista, Salete; Almeida, Jose; Lemos, Agostinho; Melo, André; Cordeiro, Maria Natália D.S.; et al. "Understanding the binding specificity of G-protein coupled receptors towards G-proteins and Arrestins: application to the dopamine receptor family". Journal of Chemical Information and Modeling (2020): http://dx.doi.org/10.1021/acs.jcim.0c00371.
    10.1021/acs.jcim.0c00371
  24. Nícia Rosário-Ferreira; António J. Preto; Rita Melo; Irina S. Moreira; Rui M. M. Brito. "The Central Role of Non-Structural Protein 1 (NS1) in Influenza Biology and Infection". International Journal of Molecular Sciences (2020): https://doi.org/10.3390/ijms21041511.
    10.3390/ijms21041511
  25. Koukos, Panagiotis I.; Roel-Touris, Jorge; Ambrosetti, Francesco; Geng, Cunliang; Schaarschmidt, Jörg; Trellet, Mikael E.; Melquiond, Adrien S. J.; et al. "An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45". Proteins: Structure, Function, and Bioinformatics 88 8 (2020): 1029-1036. http://dx.doi.org/10.1002/prot.25869.
    10.1002/prot.25869
  26. Moreira, Irina S. "Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization". Biomolecules (2019): http://dx.doi.org/10.3390/biom9110706.
    10.3390/biom9110706
  27. Beatriz Bueschbell; Carlos Barreto; António J. Preto; Anke Schiedel; Irina Moreira. "A Complete Assessment of Dopamine Receptor- Ligand Interactions through Computational Methods". Molecules (2019): https://www.mdpi.com/1420-3049/24/7/1196.
    10.3390/molecules24071196
  28. Melo, Rita; Lemos, Agostinho; Preto, Antonio J.; Almeida, Jose G.; Correia, Joao D.G.; Sensoy, Ozge; Moreira, Irina S.. "Computational Approaches in Antibody-drug Conjugate Optimization for Targeted Cancer Therapy". Current Topics in Medicinal Chemistry 18 13 (2018): 1091-1109. http://dx.doi.org/10.2174/1568026618666180731165222.
    10.2174/1568026618666180731165222
  29. Moreira, Irina Sousa; Sensoy, Ozge. "Modulation of Protein-Protein Interactions for the Development of Effective Therapeutics - From a Joint Perspective of Experiment and Computation". Current Topics in Medicinal Chemistry 18 8 (2018): 645-646. http://dx.doi.org/10.2174/156802661808180718151704.
    10.2174/156802661808180718151704
  30. Schiedel AC; Kose M; Barreto C; Bueschbell B; Morra G; Sensoy O; Moreira IS. "Prediction and Targeting of Interaction Interfaces in G-Protein Coupled Receptor Oligomers.". Current topics in medicinal chemistry (2018): http://europepmc.org/abstract/med/29866008.
    10.2174/1568026618666180604082610
  31. Lemos A; Melo R; Preto AJ; Almeida JG; Moreira IS; Dias Soeiro Cordeiro MN. "In Silico Studies Targeting G-protein Coupled Receptors for Drug Research Against Parkinson's Disease.". Current neuropharmacology (2018): http://europepmc.org/abstract/med/29521236.
    10.2174/1570159x16666180308161642
  32. Irina S. Moreira; Panagiotis I. Koukos; Rita Melo; Jose G. Almeida; Antonio J. Preto; Joerg Schaarschmidt; Mikael Trellet; et al. "SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots". Scientific Reports (2017):
    10.1038/s41598-017-08321-2
  33. Jose G. Almeida; Antonio J. Preto; Panagiotis I. Koukos; Alexandre M.J.J. Bonvin; Irina S. Moreira. "Membrane proteins structures: A review on computational modeling tools". Biochimica et Biophysica Acta (BBA) - Biomembranes 1859 10 (2017): 2021-2039. https://doi.org/10.1016/j.bbamem.2017.07.008.
    10.1016/j.bbamem.2017.07.008
  34. Moreira, Irina. "Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.". Journal of computer-aided molecular design (2017): http://europepmc.org/abstract/med/28831657.
    10.1007/s10822-017-0049-y
  35. Moreira, Irina. "Understanding the Differential Selectivity of Arrestins toward the Phosphorylation State of the Receptor.". ACS chemical neuroscience (2016): http://europepmc.org/abstract/med/27405242.
    10.1021/acschemneuro.6b00073
  36. Moreira, Irina. "A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.". International journal of molecular sciences (2016): http://europepmc.org/abstract/med/27472327.
    10.3390/ijms17081215
  37. Moreira, Irina. "General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides.". The journal of physical chemistry. A (2016): http://europepmc.org/abstract/med/27267296.
    10.1021/acs.jpca.6b02250
  38. Moreira IS. "The Role of Water Occlusion for the Definition of a Protein Binding Hot-Spot.". Current topics in medicinal chemistry (2015): http://europepmc.org/abstract/med/25986686.
    10.2174/1568026615666150519103733
  39. Munteanu, Cristian R.; Pimenta, Antonio C.; Fernandez-Lozano, Carlos; Melo, Andre; Cordeiro, Maria N. D. S.; Moreira, Irina S.. "Solvent Accessible Surface Area-Based Hot-Spot Detection Methods for Protein-Protein and Protein-Nucleic Acid Interfaces". Journal of Chemical Information and Modeling 55 5 (2015): 1077-1086. 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
  40. Oliveira, Bruno L.; Morais, Mauricio; Mendes, Filipa; Moreira, Irina S.; Cordeiro, Carlos; Fernandes, Pedro A.; Ramos, Maria J.; et al. "Re(I) and Tc(I) Complexes for Targeting Nitric Oxide Synthase: Influence of the Chelator in the Affinity for the Enzyme". Chemical Biology & Drug Design 86 5 (2015): 1072-1086. 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
  41. Moreira, Irina S.; Martins, Joao M.; Coimbra, Joa T. S.; Ramos, Maria J.; Fernandes, Pedro A.. "A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy". Physical Chemistry Chemical Physics 17 4 (2015): 2378-2387. 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
  42. Martins, Joao M.; Ramos, Rui M.; Pimenta, Antonio C.; Moreira, Irina S.. "Solvent-accessible surface area: How well can be applied to hot-spot detection?". Proteins-Structure Function and Bioinformatics 82 3 (2014): 479-490. 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
  43. Pimenta, A. C.; Fernandes, R.; Moreira, I. S.. "Evolution of drug resistance: insight on TEM ß-lactamases structure and activity and ß-lactam antibiotics". Mini Rev Med Chem 14 2 (2014): 111-22. 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
  44. Moreira, Irina S.. "Structural features of the G-protein/GPCR interactions". Biochimica Et Biophysica Acta-General Subjects 1840 1 (2014): 16-33. 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
  45. 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.. "Dynamic Structure of NGF and proNGF Complexed with p75NTR: Pro-Peptide Effect". Journal of Chemical Information and Modeling 54 7 (2014): 2051-2067. 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
  46. Moreira, Irina Sousa; Ramos, Rui Miguel; Martins, Joao Miguel; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. "Are hot-spots occluded from water?". Journal of Biomolecular Structure & Dynamics 32 2 (2014): 186-197. 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
  47. Moreira, I. S.; Martins, J. M.; Ramos, R. M.; Fernandes, P. A.; Ramos, M. J.. "Understanding the importance of the aromatic amino-acid residues as hot-spots". Biochimica Et Biophysica Acta-Proteins and Proteomics 1834 1 (2013): 404-414. 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
  48. Carneiro, J.; Duarte-Pereira, S.; Azevedo, L.; Castro, L. F. C.; Aguiar, P.; Moreira, I. S.; Amorim, A.; Silva, R. M.. "The Evolutionary Portrait of Metazoan NAD Salvage". Plos One 8 5 (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
  49. Ramos, Rui M.; Moreira, Irina S.. "Computational Alanine Scanning Mutagenesis—An Improved Methodological Approach for Protein–DNA Complexes". Journal of Chemical Theory and Computation 9 9 (2013): 4243-4256. 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
  50. Ramos, R. M.; Fernandes, L. F.; Moreira, I. S.. "Extending the applicability of the O-ring theory to protein-DNA complexes". Computational Biology and Chemistry 44 (2013): 31-39. 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
  51. Martins, Silvia A.; Perez, Marta A. S.; Moreira, Irina S.; Sousa, Sergio F.; Ramos, M. J.; Fernandes, P. A.. "Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI". Journal of Chemical Theory and Computation 9 3 (2013): 1311-1319. 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
  52. Martins, Joao M.; Ramos, Rui M.; Moreira, Irina S.. "Structural Determinants of a Typical Leucine-Rich Repeat Protein". Communications in Computational Physics 13 1 (2013): 238-255. 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
  53. Oliveira, B. L.; Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.; Santos, I.; Correia, J. D. G.. "Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms". Journal of Molecular Modeling 19 4 (2013): 1537-1551. 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
  54. Oliveira, Bruno L.; Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.; Santos, Isabel; Correia, Joao D. G.. "Theoretical studies on the binding of rhenium(I) complexes to inducible nitric oxide synthase". Journal of Molecular Graphics & Modelling 45 (2013): 13-25. 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
  55. Pimenta, A. C.; Martins, J. M.; Fernandes, R.; Moreira, I. S.. "Ligand-Induced Structural Changes in TEM-1 Probed by Molecular Dynamics and Relative Binding Free Energy Calculations". Journal of Chemical Information and Modeling 53 10 (2013): 2648-2658. 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
  56. Ribeiro, Joao V.; Cerqueira, Nuno M. F. S. A.; Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria Joao. "CompASM: an Amber-VMD alanine scanning mutagenesis plug-in". Theoretical Chemistry Accounts 131 10 (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
  57. Bach, Anders; Stuhr-Hansen, Nicolai; Thorsen, Thor S.; Bork, Nicolai; Moreira, Irina S.; Frydenvang, Karla; Padrah, Shahrokh; et al. "Structure-activity relationships of a small-molecule inhibitor of the PDZ domain of PICK1". Organic & Biomolecular Chemistry 8 19 (2010): 4281-4288. 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
  58. Thorsen, Thor S.; Madsen, Kenneth L.; Rebola, Nelson; Rathje, Mette; Anggono, Victor; Bach, Anders; Moreira, Irina S.; et al. "Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD". Proceedings of the National Academy of Sciences of the United States of America 107 1 (2010): 413-418. 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
  59. Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.. "Protein-Protein Docking Dealing With the Unknown". Journal of Computational Chemistry 31 2 (2010): 317-342. 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
  60. Moreira, Irina; Ge, Xiaoxia; Madsen, Kenneth L.; Gether, Ulrik; Weinstein, Harel. "Design and Characterization of Small Molecule Inhibitors of the PICK1 PDZ Domain with Binding Free Energy Calculations". Biophysical Journal 98 3, Supplem (2010): 428a-428a.
    http://dx.doi.org/10.1016/j.bpj.2009.12.2319
  61. Han, Yang; Moreira, Irina S.; Urizar, Eneko; Weinstein, Harel; Javitch, Jonathan A.. "Allosteric communication between protomers of dopamine class A GPCR dimers modulates activation". Nature Chemical Biology 5 9 (2009): 688-695. 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
  62. Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.. "Protein-protein recognition: a computational mutagenesis study of the MDM2-P53 complex". Theoretical Chemistry Accounts 120 4-6 (2008): 533-542. 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
  63. Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.. "Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL-10". International Journal of Quantum Chemistry 107 2 (2007): 299-310. 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
  64. Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.. "Backbone importance for protein-protein binding". Journal of Chemical Theory and Computation 3 3 (2007): 885-893. 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
  65. Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.. "Computational alanine scanning mutagenesis - An improved methodological approach". Journal of Computational Chemistry 28 3 (2007): 644-654. 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
  66. Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.. "Unravelling Hot Spots: a comprehensive computational mutagenesis study". Theoretical Chemistry Accounts 117 1 (2007): 99-113. 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
  67. Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.. "Hot spot occlusion from bulk water: A comprehensive study of the complex between the lysozyme HEL and the antibody FVD1.3". Journal of Physical Chemistry B 111 10 (2007): 2697-2706. 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
  68. Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.. "Hot spots-A review of the protein-protein interface determinant amino-acid residues". Proteins-Structure Function and Bioinformatics 68 4 (2007): 803-812. 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
  69. Moreira, Irina Sousa; Fernandes, Pedro Alexandrino; Ramos, Maria Joao. "Vascular endothelial growth factor (VEGF) inhibition - A critical review". Anti-Cancer Agents in Medicinal Chemistry 7 2 (2007): 223-245. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000244009200005&KeyUID=WOS:000244009200005.
  70. Moreira, IS; Fernandes, PA; Ramos, MJ. "Detailed microscopic study of the full ZipA : FtsZ interface". Proteins-Structure Function and Bioinformatics 63 4 (2006): 811-821. 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
  71. Moreira, IS; Fernandes, PA; Ramos, MJ. "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". Journal of Physical Chemistry B 110 22 (2006): 10962-10969. 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
  72. Moreira, IS; Fernandes, PA; Ramos, MJ. "Accuracy of the numerical solution of the Poisson-Boltzmann equation". Journal of Molecular Structure-Theochem 729 1-2 (2005): 11-18. 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
  73. Fernandes, P. A.; Carvalho, A. T. P.; Marques, A. T.; Pereira, A. L. F.; Madeira, A. P. S.; Ribeiro, A. S. P.; Carvalho, A. F. R.; et al. "New designs for MRI contrast agents". Journal of Computer-Aided Molecular Design 17 7 (2003): 463-473. http://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
Newsletter article
  1. Preto, A.J.; Matos-Filipe, Pedro; Mourão, Joana; Moreira, Irina S. "Investigadores de Coimbra desenvolvem plataforma que prevê efeito de fármacos para tratar o cancro", Notícias UC, 2022, https://www.uc.pt/fctuc/noticias/plataforma-desenvolvida-na-universidade-de-coimbra-permite-prever-efeito-da-combinacao-de-farmacos-para-tratar-o-cancro/.
Preprint
  1. "Microglia remodel the synaptic signaling required for context-dependent cognitive performance". 2021. http://dx.doi.org/10.1101/2021.10.18.464802.
    10.1101/2021.10.18.464802
Thesis / Dissertation
  1. Irina de Sousa Moreira. "Supervised Classification Applied to Hot-Spot Detection in Protein-Protein Interfaces". Master, 2016. https://repositorio-aberto.up.pt/handle/10216/97647.

Other

Dataset
  1. Moreira, Irina S. MENSAdb. http://www.moreiralab.com/resources/mensadb/.
  2. Moreira, Irina S. Dopamine Receptor. http://www.moreiralab.com/resources/dxr/.
  3. Moreira, Irina S. Spotone http://www.moreiralab.com/resources/spotone/.
  4. Moreira, Irina S. OR http://www.moreiralab.com/resources/oor/.
  5. Gomes, António José Preto Martins; Matos-Filipe, Pedro; Mourão, Joana; Moreira, Irina S. SynPred - http://www.moreiralab.com/resources/synpred/.
  6. HOOKED.
  7. SicknessMiner.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022 Artificial intelligence applied to drug discovery AGM meeting 2022 ELIXIR 3D-BioInfo Community in Structural Bioinformatics
(United Kingdom)
2021/10 Application of artificial intelligence to structural-functional biology and drug design BioSolveIT Webinars
BioSolveIT (Germany)
2021/04 Exploring the GPCR interactome using computational and data-driven approaches European research network in signal transduction Meeting
ERNEST COST ACTION
2019/10 How artificial intelligence and big data can be applied to GPCR functional understanding European research network in signal transduction,
(Belfast, Ireland)
2019 Structural biology and AI- a new partnership New diagnostic and therapeutic tools against multidrug resistant tumours WG1 meeting
(Vienna)
2019 Artificial intelligence application to structural biology BMBF-BIGS-DrugS Kolloquium/Pharmazeutisches Kolloquium
Bonn University (Germany)
2019 How artificial intelligence is changing structural biology National Encounter of Biochemistry Students, Aveiro, Portugal
2019 Artificial intelligence application to drug development
53rd Annual Scientific Meeting of the European society for clinical investigation, Coimbra, Portugal
2019 Structural biology and AI- a new hope Universidade do Minho, Braga, Portugal
2019 Structural biology and AI- a new partnership I Portuguese Biomedical Engineering Summit (BES), Lisbon, Portugal.
2019 Application of artificial intelligence to structural biology Meeting about intelligent strategies for computer chemistry, Coimbra, Portugal.
2017 Characterization of binding interface determinants Netherlands Society of Biomolecular Modeling, Utrecht, Netherlands
2017 Protein-protein interactions: a structural perspective of functionally important mutations EMBO Workshop on Integrating genomics and biophysics to comprehend functional genetic variation, Turin, Italy.
2017 SpotON: a machine learning approach for binding hot-spot determination Biophysical Society Meeting, New Orleans, USA
2015 Structural/energetic analysis of protein-based interactions: highlighting the electrostatics contributions MBI workshop: Multiple Faces of Biomolecular Electrostatics, USA.
2015 Insights into the plasticity and adaptability of protein-protein interfaces 25th Intl. BIOMOS Symposium on Biomolecular Simulation, Ausserberg, Switzerland.
2014 The role of electrostatics in the prediction of binding hot-spots Protein Electrostatics Satellite Meeting, Lisbon, Portugal.
2011 Protein-protein interfacial studies 5th Theoretical Biophysics International Symposium, Funchal, Portugal.
2011 The role of electrostatics in biological systems Modelling Electrostatics in Molecular Biology, Clemson, USA.
2010 Docking studies and molecular dynamics simulations of Re (I) complexes containing L-Arg derivatives for iNOS targeting Medicinal Chemistry Meeting, Coimbra, Portugal.
2006 Computational alanine scanning mutagenesis: application to a wide range of biological systems International School of Physics “E. Fermi”, “Protein Folding and Drug Design”, Varenna, Italy.

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2021 - Current Artificial intelligence Application to Structural Biology
Supervisor
 Biochemistry (Degree)
Universidade de Coimbra, Portugal
2021 - Current The Interaction between Stargazin and Kv7.2 and its Association with Psychiatric Disorders
Supervisor
 Doutoramento em Biociencias (PhD)
Universidade de Coimbra, Portugal
2021 - Current Pluridimensional signaling of GPCR - understanding mutagenesis effect on specific receptorsome selection
Supervisor
 Doutoramento em Biociencias (PhD)
Universidade de Coimbra, Portugal
2021 - Current Protein-ligand – a better understanding using AI algorithms
Supervisor
 Mestrado em Biologia Computacional (Master)
Universidade de Coimbra, Portugal
2021 - Current Understanding GPCR mediated interactions
Supervisor
 Master's Degree in Cellular and Molecular Biology (Master)
Universidade de Coimbra, Portugal
2021 - Current Development of a new method to detect anti-microbial peptides
Supervisor
 Master´s Degree in Biomedical Research (Master)
Universidade de Coimbra, Portugal
2021 - Current Predicting cellular OMIC responses through machine learning
Supervisor
 Master's Degree in Cellular and Molecular Biology
Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2020/10 - Current Drug-Target Interaction Prediction
Supervisor
 Mestrado de Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Desporto, Portugal
2020/09 - Current Cutting-Edge Virus-Host Interactome Discovery: A Multi-Omics AI Driven Approach
Supervisor
 PhD programme in experimental Biology and biomedicine (PhD) (PhD)
Universidade de Coimbra, Portugal
2020 - Current Characterization of protein-protein interactions involving G-protein coupled receptor 143 by computational and pharmacological methods
Supervisor of Beatriz Theresa Ruth Bueschbell
 PhD programme in experimental Biology and biomedicine (PhD)
Universidade de Coimbra, Portugal
2019 - Current Applying computational tools to the study of GPCRs structure and dynamics
Supervisor
 PhD programme in experimental Biology and biomedicine (PhD)
Universidade de Coimbra, Portugal
2018 - Current Deep-learning application to in silico drug design
Supervisor of António José Preto Martins Gomes
 PhD programme in experimental Biology and biomedicine (PhD)
Universidade de Coimbra, Portugal
2017 - Current Exploring protein-protein and protein-RNA interactions in influenza virus non-structural protein 1 (NS1)
Co-supervisor of Nicia Filipa Rosario-Ferreira
 Chemistry (PhD)
Universidade de Coimbra, Portugal
2020/08 - 2021/11 SARS-CoV-2 characterisation – an in-silico approach
Supervisor
 Biochemistry (Master)
Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2021 - 2021 In silico application to Omics
Supervisor
 Biology (Degree)
Universidade de Coimbra, Portugal
2020/09 - 2021 Sars-Cov-2 membrane protein: from genomic data to structural new insights
Supervisor
 Bioinformatics and Computational Biology (Master)
Universidade do Porto, Portugal
2019/09 - 2021 Prediction of Cancer Cell Resistance to Therapy
Supervisor
 Bioinformatics (Master)
Universidade de Trás-os-Montes e Alto Douro, Portugal
2019 - 2021 Decoding Partner Specificity in Opioid Receptor Family
Supervisor
 Biochemistry Master (Master)
Universidade de Coimbra, Portugal
2019/09 - 2020 The Effects of CACNG2 Mutations in Psychiatric Disorders
Supervisor
 Cellular and Molecular Biology (Master)
Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2019/02 - 2019/07 Text-mining for the discovery of novel haematological cancer biomarkers
Supervisor
 Biochemistry (Degree)
Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2018/09 - 2019/07 A Computational Method to Predict the Combinatory Effect of Drugs in Cancer
Supervisor
 Pharmaceutical Biotechnology (Master)
Universidade de Coimbra Faculdade de Farmácia, Portugal
2017/09 - 2018/07 Applying computational tools to the study of GPCRs structure and dynamics
Supervisor of Carlos André Viegas Barreto
 Cellular and Molecular Biology (Master)
Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2016/09 - 2017/09 A bioinformatics approach for the understanding of membrane protein complexes
Supervisor
 Biochemistry (Master)
Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2016/09 - 2017/09 Computational methods for the understanding of protein-based interactions
Supervisor
 Cellular and Molecular Biology (Master)
Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2012/09 - 2013/07 Study of protein-nucleic acid complexes
Co-supervisor
 Chemistry (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2011/09 - 2012/07 Determinação computacional dos efeitos da mutagénese em interfaces proteína- dna
Co-supervisor
 Biochemistry (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2011/09 - 2012 Biochemical and structural characterization of b-lactamases TEM-180 and TEM-201
Supervisor
 Biochemical Health Technology (Master)
Instituto Politécnico do Porto Escola Superior de Saúde, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2022 - Current BioData.pt Talks – 3D BioTalks” (2022)
Conference (Member of the Organising Committee)
2021 - 2021 GROMACS Workshop - https://www.eventbrite.pt/e/bilhetes-gromacs-workshop-162032753327 (2021 - 2021)
Workshop (Co-organisor)
 Universidade de Coimbra, Portugal
2016 - 2021 Scientific Committee of MOL2NET, International Conference of Multidisciplinary Sciences. (2016 - 2021)
Conference
2013 - 2021 MEETING OF YOUNG RESEARCHERS IN STRUCTURAL COMPUTATIONAL BIOLOGY The Meeting of Young Researchers in Structural Computational Biology (EJIBCE) aims at bringing together the Portuguese scientific community working in the field in a free-of-charge meeting, to provide a forum for discussion and sharing with no strings attached. (2013 - 2020)
Conference (President of the Organising Committee)

Committee member

Activity description
Role 		Institution / Organization
2020/09 - Current Master in Computational Biology
Coordinator
 Universidade de Coimbra Departamento de Ciências da Vida, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2022 - Current Molecular systems biology Masters in Computational Biology (Mestrado) Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2022 - Current Computational drug discovery Masters in Computational Biology Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2020/02 - Current Introduction to Structural Biochemistry Biochemistry (Licenciatura) Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2020 - Current Applied Omics Computational Biology (Mestrado) Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2020 - Current Biological Data Analysis Computational Biology (Mestrado) Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2020 - Current Biochemistry Chemistry (Licenciatura) Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2019/09 - Current Biochemistry of Proteins, Nucleic Acids and Lipids Biochemistry (Licenciatura) Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2017 - Current Computational biology (Doutoramento) Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
2019/09 - 2020/02 Introduction to Biology Biochemistry (Licenciatura) Universidade de Coimbra Departamento de Ciências da Vida, Portugal
2018 - 2018 Invited lecturer at Infection course of the BEB PhD programme (Doutoramento)
2018 - 2018 Invited lecturer at Therapeutics course of the BEB PhD programme (Doutoramento)
2018 - 2018 Computational Analysis of Proteomes and Genomes Class of Biostatistics and Bioinformatics applied to Health Master Program - Polytechnic Institute of Porto, Portugal (Mestrado)

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2022/10/31 Investigadores de Coimbra desenvolvem plataforma que prevê efeito de fármacos para tratar o cancro Expresso
2022/10/31 Investigadores de Coimbra desenvolvem plataforma que prevê efeito de fármacos para tratar o cancro Observador
2022/05/05 Cientistas de Coimbra descobrem alterações cognitivas provocadas por variante genética Expresso
2022/03/15 Study models SARS-CoV-2 M protein monomer and dimer 3D structures news-medical.net
2022/02/01 Eurocc.FCCN case studies publication FCCN
2021/10/27 Projeto sobre doenças neurológicas vence prémio da Agência Nacional de Inovação Observador
2021 mRNA Núcleo de Estudantes de Bioquímica Interview RNA Mensageiro Magazine from Biochemistry Students @UC
2020/11/05 Cientistas usam dados e inteligência artificial para combater pandemia RTP Online
2020/11/05 Covid-19: Cientistas usam dados e inteligência artificial para combater pandemia Visao
2020/11/05 Cientistas da Universidade de Coimbra usam dados e inteligência artificial para combater pandemia Observador
2020/09/15 Universidade de Coimbra recebe 782 mil euros para estudo sobre epilepsia RTP

Journal scientific committee

Journal title (ISSN) Publisher
2020 - Current International Journal of Molecular Sciences Topics Editor (1422-0067) MDPI AG
2020 - Current Biochem - Editorial Board Member MDPI
2021 - 2022 Frontiers in Pharmacology
2019 - 2021 Methods in Molecular Biology Invited Editor Springer
2017 - 2019 Molecules Invited Editor (1420-3049) MDPI AG
2017 - 2018 Current Topics of Medicinal Chemistry Invited Editor
Distinctions

Award

2023 RCE+ awards five awards to young entrepreneurship projects
Região de Coimbra Empreende+, Portugal
2023 Ineo start Acceleration Program
Instituto Pedro Nunes, Portugal
2021 Born from Knowledge 2021 "Health and Wellbeing"
Agência Nacional de Inovação SA, Portugal
2014 Committee for Professional Opportunities for Women Travel Award
2008 Luso-American Foundation Network Grant (FLAD)
Fundação Luso-Americana, Portugal
2003 Eng. António de Almeida's Prize - For the top-ranking student in the Biochemistry Degree.
2003 PhD Fellowship
Fundação para a Ciência e a Tecnologia, Portugal
1998 Excellence Prize - For the top-ranking student in the Secondary School.

Other distinction

2024 InvestEU Portal e-Pitch – Women entrepreneurs – one of the five selected at the European level.
Bpifrance, France
2023 Nomeação Prémio activa mulheres Inspiradoras
Activa, Portugal
2022 Selected for HiTech 2022 program
2022 BfK Acceleration Program: INNOV@RISE
Agência Nacional de Inovação SA, Portugal
2019 Assistant Professor at Data Science/Computer Science Department of Science and technology Faculty of University of Coimbra; tenure-track position attained in an international competitive call; declined in favor of similar position at Life Sciences Dep
2019 Scientific Employment Stimulus Position CEECIND/03938/2018 - Assistant Professor - attained in an international highly competitive FCT call; declined in favor of assistant professor position at Life Sciences Department
Fundação para a Ciência e a Tecnologia, Portugal
2018 Interview Stage ERC starting grant - LS7 pannel
European Research Council, Belgium
2015 Marie Sklodowska-Curie Individual Fellowship MSCA-IF-2015 (MEMBRANEPROT 659826)
European Commission, Belgium
2015 FCT Individual Postdoctoral Fellowship SFRH/BPD/104128/2014 - declined
Fundação para a Ciência e a Tecnologia, Portugal
2006 MGMS Registration Fellowship - Quantum Pharmacology - 30 years on, Oxford, UK
2006 NBCR Summer Institute Travel and Registration Fellowship - NBCR Summer Institute: Cyberinfrastructure & Multiscale Modeling Approaches”, La Jolla, California
2006 Marie Curie Travel and Registration Fellowship - CCP5 and Marie Curie Actions: Methods in Molecular Simulation Summer School 2006”, University of Cardiff, Wales.
2006 Italian Physical Society Scholarship - International School of Physics “E. Fermi”, “Protein Folding and Drug Design”, Varenna, Italy.
2006 EMBO Fellowship – “Biomolecular simulation - an EMBO course”, Paris, France.