LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking. - José Luis Velázquez-Libera; Fabio Durán-Verdugo; Alejandro Valdés-Jiménez; Gabriel Núñez-Vivanco; Julio Caballero (Bioinform., 2020)

Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition. - José Luis Velázquez-Libera; Julio Caballero; Jans H. Alzate-Morales; Jose Javier Ruiz-Pernía; Iñaki Tuñón (J. Chem. Inf. Model., 2024)

CorrEA: A Web Server for Optimizing Correlations between Calculated Energies and Activities in Ligand-Receptor Systems Considering Multiple Binding Site Conformations. - Sergio Alfaro; Fabián González-Norambuena; José Luis Velázquez-Libera; Francisco Adasme-Carreño; Julio Caballero (J. Chem. Inf. Model., 2025)