Screened Charge Electrostatic Model in Protein-Protein Docking Simulations. - Juan Fernández-Recio; Maxim Totrov; Ruben Abagyan (Pacific Symposium on Biocomputing, 2002)

Optimized Desolvation for Rigid-Body Docking: Fast Prediction of Protein Interaction Sites. - Juan Fernández-Recio (Spanish Bioinformatics Conference, 2004)

Predicting Protein-Protein Interface using Desolvation Energy Similarity Matching. - Yasir Arafat; Gour C. Karmakar; Joarder Kamruzzaman; Juan Fernández-Recio (CIBCB, 2006)

Structural assembly of two-domain proteins by rigid-body docking. - Tammy M. K. Cheng; Tom L. Blundell; Juan Fernández-Recio (BMC Bioinform., 2008)

In silico docking of urokinase plasminogen activator and integrins. - Bernard Degryse; Juan Fernández-Recio; Valentina Citro; Francescol Blasi; Maria Vittoria Cubellis (BMC Bioinform., 2008)

Identification of hot-spot residues in protein-protein interactions by computational docking. - Solène Grosdidier; Juan Fernández-Recio (BMC Bioinform., 2008)

FRODOCK: a new approach for fast rotational protein-protein docking. - José Ignacio Garzón; José Ramón López-Blanco; Carles Pons; Julio A. Kovacs; Ruben Abagyan; Juan Fernández-Recio; Pablo Chacón (Bioinform., 2009)

Predicting protein - protein interfaces as clusters of Optimal Docking Area points. - Yasir Arafat; Joarder Kamruzzaman; Gour C. Karmakar; Juan Fernández-Recio (Int. J. Data Min. Bioinform., 2009)

Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments. - Roberto Mosca 002; Carles Pons; Juan Fernández-Recio; Patrick Aloy (PLoS Comput. Biol., 2009)

Drug Design on the Cell BE. - Cecilia González-Alvarez; Harald Servat; Daniel Cabrera-Benitez; Xavier Aguilar; Carles Pons; Juan Fernández-Recio; Daniel Jiménez-González (Scientific Computing with Multicore and Accelerators, 2010)

Structural Prediction of Protein-RNA Interaction by Computational Docking with Propensity-Based Statistical Potentials. - Laura Perez-Cano; Albert Solernou 001; Carles Pons; Juan Fernández-Recio (Pacific Symposium on Biocomputing, 2010)

Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation. - Albert Solernou 001; Juan Fernández-Recio (BMC Bioinform., 2010)

Prediction of protein-binding areas by small-world residue networks and application to docking. - Carles Pons; Fabian Glaser; Juan Fernández-Recio (BMC Bioinform., 2011)

Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking. - Carles Pons; David Talavera; Xavier de la Cruz; Modesto Orozco; Juan Fernández-Recio (J. Chem. Inf. Model., 2011)

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models. - Iain H. Moal; Juan Fernández-Recio (Bioinform., 2012)

Cell-Dock: high-performance protein-protein docking. - Carles Pons; Daniel Jiménez-González; Cecilia González-Alvarez; Harald Servat; Daniel Cabrera-Benitez; Xavier Aguilar; Juan Fernández-Recio (Bioinform., 2012)

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)

SwarmDock: a server for flexible protein-protein docking. - Mieczyslaw Torchala; Iain H. Moal; Raphael A. G. Chaleil; Juan Fernández-Recio; Paul A. Bates (Bioinform., 2013)

The scoring of poses in protein-protein docking: current capabilities and future directions. - Iain H. Moal; Mieczyslaw Torchala; Paul A. Bates; Juan Fernández-Recio (BMC Bioinform., 2013)

Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization. - Rudi Agius; Mieczyslaw Torchala; Iain H. Moal; Juan Fernández-Recio; Paul A. Bates (PLoS Comput. Biol., 2013)

Comment on 'protein-protein binding affinity prediction from amino acid sequence'. - Iain H. Moal; Juan Fernández-Recio (Bioinform., 2015)

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)

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

UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes. - Pep Amengual-Rigo; Juan Fernández-Recio; Victor Guallar (Bioinform., 2021)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)