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Journal of Computer-Aided Molecular Design|October 18, 2022
Protocol for iterative optimization of modified peptides bound to protein targetsRodrigo Ochoa, Pilar Cossio, Thomas FoxMolecules (Basel, Switzerland)|April 3, 2021
PepFun: Open Source Protocols for Peptide-Related Computational AnalysisRodrigo Ochoa, Pilar CossioJournal of Chemical Information and Modeling|July 11, 2019
Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics SimulationsRodrigo Ochoa, Alessandro Laio, Pilar CossioPhysical Chemistry Chemical Physics : PCCP|October 6, 2018
Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acidsRodrigo Ochoa, Miguel A Soler, Alessandro Laio, et al.Journal of Molecular Graphics & Modelling|September 2, 2023
Assessing the fast prediction of peptide conformers and the impact of non-natural modificationsRodrigo Ochoa, Thomas FoxFrontiers in Molecular Biosciences|July 5, 2021
Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide BindersRodrigo Ochoa, Roman A Laskowski, Janet M Thornton, et al.Computational and Structural Biotechnology Journal|March 9, 2023
Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark studyRodrigo Ochoa, Thyago R Cardim-Pires, Ricardo Sant'Anna, et al.BMC Bioinformatics|December 30, 2020
An automated protocol for modelling peptide substrates to proteasesRodrigo Ochoa, Mikhail Magnitov, Roman A Laskowski, et al.Frontiers in Immunology|May 16, 2022
Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution ProtocolRodrigo Ochoa, Victoria Alves Santos Lunardelli, Daniela Santoro Rosa, et al.Journal of Cheminformatics|September 12, 2023
pyPept: a python library to generate atomistic 2D and 3D representations of peptidesRodrigo Ochoa, J B Brown, Thomas FoxPageof 20