New designs for MRI contrast agents. - Pedro Alexandrino Fernandes; Alexandra T. P. Carvalho; A. T. Marques; A. L. F. Pereira; A. P. S. Madeira; Ana Sofia P. Ribeiro; A. F. R. Carvalho; E. T. A. Ricardo; F. J. V. Pinto; Hélder A. Santos; H. D. G. Mangericão; H. M. Martins; et al. (J. Comput. Aided Mol. Des., 2003)

Computational alanine scanning mutagenesis - An improved methodological approach. - Irina S. Moreira; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Chem., 2007)

Protein-protein docking dealing with the unknown. - Irina S. Moreira; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Chem., 2010)

Extending the applicability of the O-ring theory to protein-DNA complexes. - R. M. Ramos; L. F. Fernandes; Irina S. Moreira (Comput. Biol. Chem., 2013)

Ligand-Induced Structural Changes in TEM-1 Probed by Molecular Dynamics and Relative Binding Free Energy Calculations. - António César Pimenta; João M. Martins; Ruben Fernandes; Irina S. Moreira (J. Chem. Inf. Model., 2013)

Dynamic Structure of NGF and proNGF Complexed with p75NTR: Pro-Peptide Effect. - António César Pimenta; Daniel F. A. R. Dourado; João M. Martins; André Melo; M. N. Dias Soeiro Cordeiro; Ramiro D. Almeida; Giulia Morra; Irina S. Moreira (J. Chem. Inf. Model., 2014)

Solvent Accessible Surface Area-Based Hot-Spot Detection Methods for Protein-Protein and Protein-Nucleic Acid Interfaces. - Cristian R. Munteanu; António César Pimenta; Carlos Fernandez-Lozano; André Melo; M. N. D. S. Cordeiro; Irina S. Moreira (J. Chem. Inf. Model., 2015)

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. - Zeynep Kurkcuoglu; Panagiotis I. Koukos; Nevia Citro; Mikael E. Trellet; João P. G. L. M. Rodrigues; Irina S. Moreira; Jorge Roel-Touris; Adrien S. J. Melquiond; Cunliang Geng; Jörg Schaarschmidt; Li C. Xue; Anna Vangone; et al. (J. Comput. Aided Mol. Des., 2018)

Understanding the Binding Specificity of G-Protein Coupled Receptors toward G-Proteins and Arrestins: Application to the Dopamine Receptor Family. - António J. Preto; Carlos A. V. Barreto; Salete J. Baptista; José G. de Almeida; Agostinho Lemos; André Melo; M. Natália Dias Soeiro Cordeiro; Zeynep Kurkcuoglu; Rita Melo; Irina S. Moreira (J. Chem. Inf. Model., 2020)

Predicting Hot Spots Using a Deep Neural Network Approach. - António J. Preto; Pedro Matos-Filipe; José G. de Almeida; Joana Mourão; Irina S. Moreira (Artificial Neural Networks, 3rd Edition, 2021)

MENSAdb: a thorough structural analysis of membrane protein dimers. - Pedro Matos-Filipe; António J. Preto; Panagiotis I. Koukos; Joana Mourão; Alexandre M. J. J. Bonvin; Irina S. Moreira (Database J. Biol. Databases Curation, 2021)

SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations. - Nícia Rosário-Ferreira; Victor Guimarães 001; Vítor Santos Costa; Irina S. Moreira (BMC Bioinform., 2021)

DrugTax: package for drug taxonomy identification and explainable feature extraction. - António J. Preto; Paulo C. Correia; Irina S. Moreira (J. Cheminformatics, 2022)

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 (Bioinform., 2023)

Call for Papers: Data Generation in Healthcare Environments. - Ricardo Cardoso Pereira; Pedro Pereira Rodrigues; Irina S. Moreira; Pedro Henriques Abreu (J. Biomed. Informatics, 2024)

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 (J. Chem. Inf. Model., 2024)

POSEIDON: Peptidic Objects SEquence-based Interaction with cellular DOmaiNs: a new database and predictor. - António J. Preto; Ana B. Caniceiro; Francisco Duarte; Hugo Fernandes; Lino Ferreira; Joana Mourão; Irina S. Moreira (J. Cheminformatics, 2024)

GPCR-A17 MAAP: mapping modulators, agonists, and antagonists to predict the next bioactive target. - Ana B. Caniceiro; Ana M. B. Amorim; Nícia Rosário-Ferreira; Irina S. Moreira (J. Cheminformatics, 2025)