myChEMBL: a virtual machine implementation of open data and cheminformatics tools. - Rodrigo Ochoa; Mark Davies; George Papadatos; Francis Atkinson; John P. Overington (Bioinform., 2014)

Drug search for leishmaniasis: a virtual screening approach by grid computing. - Rodrigo Ochoa; Stanley J. Watowich; Andrés F. Flórez; Carol V. Mesa; Sara M. Robledo; Carlos Muskus (J. Comput. Aided Mol. Des., 2016)

Repurposing of known drugs for leishmaniasis treatment using bioinformatic predictions, in vitro validations and pharmacokinetic simulations. - Christian Bustamante; Rodrigo Ochoa; Claudia Asela; Carlos Muskus (J. Comput. Aided Mol. Des., 2019)

Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations. - Rodrigo Ochoa; Alessandro Laio; Pilar Cossio (J. Chem. Inf. Model., 2019)

An automated protocol for modelling peptide substrates to proteases. - Rodrigo Ochoa; Mikhail D. Magnitov; Roman A. Laskowski; Pilar Cossio; Janet M. Thornton (BMC Bioinform., 2020)

PARCE: Protocol for Amino acid Refinement through Computational Evolution. - Rodrigo Ochoa; Miguel A. Soler; Alessandro Laio; Pilar Cossio (Comput. Phys. Commun., 2021)

Protocol for iterative optimization of modified peptides bound to protein targets. - Rodrigo Ochoa; Pilar Cossio; Thomas Fox (J. Comput. Aided Mol. Des., 2022)

BILN: A Human-Readable Line Notation for Complex Peptides. - Thomas Fox; Michael Bieler; Peter Haebel; Rodrigo Ochoa; Stefan Peters; Alexander Weber 002 (J. Chem. Inf. Model., 2022)

pyPept: a python library to generate atomistic 2D and 3D representations of peptides. - Rodrigo Ochoa; J. B. Brown; Thomas Fox (J. Cheminformatics, 2023)