KoBaMIN: a knowledge-based minimization web server for protein structure refinement. - João P. G. L. M. Rodrigues; Michael Levitt 001; Gaurav Chopra (Nucleic Acids Res., 2012)

HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors. - Panagiotis L. Kastritis; João P. G. L. M. Rodrigues; Alexandre M. J. J. Bonvin (J. Chem. Inf. Model., 2014)

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. - Li C. Xue; João P. G. L. M. Rodrigues; Panagiotis L. Kastritis; Alexandre M. J. J. Bonvin; Anna Vangone (Bioinform., 2016)

Template-based protein-protein docking exploiting pairwise interfacial residue restraints. - Li C. Xue; João P. G. L. M. Rodrigues; Drena Dobbs; Vasant G. Honavar; Alexandre M. J. J. Bonvin (Briefings Bioinform., 2017)

pdb-tools: a swiss army knife for molecular structures. - João P. G. L. M. Rodrigues; João M. C. Teixeira; Mikaël Trellet; Alexandre M. J. J. Bonvin (F1000Research, 2018)

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)

Insights on cross-species transmission of SARS-CoV-2 from structural modeling. - João P. G. L. M. Rodrigues; Susana Barrera-Vilarmau; João M. C. Teixeira; Marija Sorokina; Elizabeth Seckel; Panagiotis L. Kastritis; Michael Levitt 001 (PLoS Comput. Biol., 2020)

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. - Peter K. Eastman; Raimondas Galvelis; Raúl P. Peláez; Charlles R. A. Abreu; Stephen E. Farr; Emilio Gallicchio; Anton Gorenko; Michael M. Henry; Frank Hu; Jing Huang 004; Andreas Krämer; Julien Michel; et al. (CoRR, 2023)