Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions. - Ramon Aragues; Andrej Sali; Jaume Bonet; Marc A. Martí-Renom; Baldo Oliva (PLoS Comput. Biol., 2007)

iLoops: a protein-protein interaction prediction server based on structural features. - Joan Planas-Iglesias; Manuel Alejandro Marín-López; Jaume Bonet; Javier García-García 002; Baldo Oliva (Bioinform., 2013)

Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications. - Jaume Bonet; András Fiser; Baldo Oliva; Narcis Fernandez-Fuentes (Bio Algorithms Med Syst., 2014)

Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design. - Jaume Bonet; Joan Segura; Joan Planas-Iglesias; Baldomero Oliva; Narcis Fernandez-Fuentes (Bioinform., 2014)

ArchDB 2014: structural classification of loops in proteins. - Jaume Bonet; Joan Planas-Iglesias; Javier García-García 002; Manuel Alejandro Marín-López; Narcis Fernandez-Fuentes; Baldo Oliva (Nucleic Acids Res., 2014)

On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. - Manuel Alejandro Marín-López; Joan Planas-Iglesias; Joaquim Aguirre-Plans; Jaume Bonet; Javier García-García 002; Narcis Fernandez-Fuentes; Baldo Oliva (Bioinform., 2018)

Rosetta FunFolDes - A general framework for the computational design of functional proteins. - Jaume Bonet; Sarah Wehrle; Karen Schriever; Che Yang; Anne Billet; Fabian Sesterhenn; Andreas Scheck; Freyr Sverrisson; Barbora Veselkova; Sabrina Vollers; Roxanne Lourman; Mélanie Villard; et al. (PLoS Comput. Biol., 2018)

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics. - Jaume Bonet; Zander Harteveld; Fabian Sesterhenn; Andreas Scheck; Bruno E. Correia (BMC Bioinform., 2019)

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions. - Joaquim Aguirre-Plans; Alberto Meseguer; Ruben Molina-Fernandez; Manuel Alejandro Marín-López; Gaurav Jumde; Kevin Casanova; Jaume Bonet; Oriol Fornes; Narcis Fernandez-Fuentes; Baldo Oliva (BMC Bioinform., 2021)

RosettaSurf - A surface-centric computational design approach. - Andreas Scheck; Stéphane Rosset; Michaël Defferrard; Andreas Loukas; Jaume Bonet; Pierre Vandergheynst; Bruno E. Correia (PLoS Comput. Biol., 2022)

SBILib: a handle for protein modeling and engineering. - Patrick Gohl; Jaume Bonet; Oriol Fornes; Joan Planas-Iglesias; Narcis Fernandez-Fuentes; Baldo Oliva (Bioinform., 2023)