SRide: a server for identifying stabilizing residues in proteins. - Csaba Magyar; M. Michael Gromiha; Gerard Pujadas; Gábor E. Tusnády; István Simon (Nucleic Acids Res., 2005)

BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock. - Montserrat Vaqué; Anna Arola; Carles Aliagas; Gerard Pujadas (Bioinform., 2006)

Structural insights for the design of new PPARgamma partial agonists with high binding affinity and low transactivation activity. - Laura Guasch; Esther Sala; Cristina Valls; Mayte Blay; Miquel Mulero; Lluís Arola; Gerard Pujadas; Santiago Garcia-Vallvé (J. Comput. Aided Mol. Des., 2011)

DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets. - Adrià Cereto-Massagué; Laura Guasch; Cristina Valls; Miquel Mulero; Gerard Pujadas; Santiago Garcia-Vallvé (Bioinform., 2012)

DecoyFinder, a tool for finding decoy molecules. - Adrià Cereto-Massagué; Santiago Garcia-Vallvé; Gerard Pujadas (J. Cheminformatics, 2012)

The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. - Adrià Cereto-Massagué; María José Ojeda; Robbie P. Joosten; Cristina Valls; Miquel Mulero; M. Josepa Salvado; Anna Arola-Arnal; Lluís Arola; Santiago Garcia-Vallvé; Gerard Pujadas (J. Cheminformatics, 2013)

Challenges in distinguishing functional proteins from polyproteins in databases: implications for drug discovery. - Ariadna Llop-Peiró; Gerard Pujadas; Santiago Garcia-Vallvé (Briefings Bioinform., 2024)

Correction: DecoyFinder, a tool for finding decoy molecules. - Adrià Cereto-Massagué; Santiago Garcia-Vallvé; Gerard Pujadas (J. Cheminformatics, 2024)

SARS-CoV-2 main protease (M-pro) mutational profiling: An insight into mutation coldspots. - Pol Garcia-Segura; Ariadna Llop-Peiró; Nil Novau-Ferré; Júlia Mestres-Truyol; Bryan Saldivar-Espinoza; Gerard Pujadas; Santiago Garcia-Vallvé (Comput. Biol. Medicine, 2025)