pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring. - Brian Jiménez-García; Carles Pons; Juan Fernández-Recio (Bioinform., 2013)

CCharPPI web server: computational characterization of protein-protein interactions from structure. - Iain H. Moal; Brian Jiménez-García; Juan Fernández-Recio (Bioinform., 2015)

pyDockSAXS: protein-protein complex structure by SAXS and computational docking. - Brian Jiménez-García; Carles Pons; Dmitri I. Svergun; Pau Bernadó; Juan Fernández-Recio (Nucleic Acids Res., 2015)

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection. - Iain H. Moal; Didier Barradas-Bautista; Brian Jiménez-García; Mieczyslaw Torchala; Arjan van der Velde; Thom Vreven; Zhiping Weng; Paul A. Bates; Juan Fernández-Recio (Bioinform., 2017)

LightDock: a new multi-scale approach to protein-protein docking. - Brian Jiménez-García; Jorge Roel-Touris; Miguel Romero-Durana; Miquel Vidal; Daniel Jiménez-González; Juan Fernández-Recio (Bioinform., 2018)

SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. - Justina Jankauskaite; Brian Jiménez-García; Justas Dapkunas; Juan Fernández-Recio; Iain H. Moal (Bioinform., 2019)

PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes. - Brian Jiménez-García; Katarina Elez; Panagiotis I. Koukos; Alexandre M. J. J. Bonvin; Anna Vangone (Bioinform., 2019)

proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking. - Francesco Ambrosetti; Tobias Hegelund Olsen; Pier Paolo Olimpieri; Brian Jiménez-García; Edoardo Milanetti; Paolo Marcatili; Alexandre M. J. J. Bonvin (Bioinform., 2020)

LightDock goes information-driven. - Jorge Roel-Touris; Alexandre M. J. J. Bonvin; Brian Jiménez-García (Bioinform., 2020)

pyDockEneRes: per-residue decomposition of protein-protein docking energy. - Miguel Romero-Durana; Brian Jiménez-García; Juan Fernández-Recio (Bioinform., 2020)

Structural biology in the clouds: The WeNMR-EOSC Ecosystem. - Rodrigo Vargas Honorato; Panagiotis I. Koukos; Brian Jiménez-García; Andrei Tsaregorodtsev; Marco Verlato; Andrea Giachetti 002; Antonio Rosato; Alexandre M. J. J. Bonvin (CoRR, 2021)

The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions. - Brian Jiménez-García; Jorge Roel-Touris; Didier Barradas-Bautista (Nucleic Acids Res., 2023)

UDock2: interactive real-time multi-body protein-protein docking software. - Cyprien Plateau-Holleville; Simon Guionnière; Benjamin Boyer; Brian Jiménez-García; Guillaume Levieux; Stéphane Mérillou; Maxime Maria; Matthieu Montès (Bioinform., 2023)

Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking. - Gilberto Pereira; Brian Jiménez-García; Riccardo Pellarin; Guillaume Launay; Sangwook Wu; Juliette Martin; Paulo C. T. Souza (J. Chem. Inf. Model., 2023)

HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes. - Marco Giulini; Victor Reys; João M. C. Teixeira; Brian Jiménez-García; Rodrigo V. Honorato; Anna Kravchenko; Xiaotong Xu; Raphaëlle Versini; Anna Engel; Stefan Verhoeven; Alexandre M. J. J. Bonvin (J. Chem. Inf. Model., 2025)