Genetic neural network modeling of the selective inhibition of the intermediate-conductance Ca2+-activated K+ channel by some triarylmethanes using topological charge indexes descriptors. - Julio Caballero; Miguel Garriga; Michael Fernández (J. Comput. Aided Mol. Des., 2005)

Modeling of Cyclin-Dependent Kinase Inhibition by 1H-Pyrazolo[3, 4-d]Pyrimidine Derivatives Using Artificial Neural Network Ensembles. - Michael Fernández; Alain Tundidor-Camba; Julio Caballero (J. Chem. Inf. Model., 2005)

Amino Acid Sequence Autocorrelation Vectors and Ensembles of Bayesian-Regularized Genetic Neural Networks for Prediction of Conformational Stability of Human Lysozyme Mutants. - Julio Caballero; Leyden Fernández; José Ignacio Abreu; Michael Fernández (J. Chem. Inf. Model., 2006)

Insights into the Structural Basis of N2 and O6 Substituted Guanine Derivatives as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors: Prediction of the Binding Modes and Potency of the inhibitors by Docking and ONIOM Calculations. - Jans H. Alzate-Morales; Julio Caballero; Ariela Vergara Jaque; Fernando D. González Nilo (J. Chem. Inf. Model., 2009)

Computational Study of the Interactions between Guanine Derivatives and Cyclin-Dependent Kinase 2 (CDK2) by CoMFA and QM/MM. - Jans H. Alzate-Morales; Julio Caballero (J. Chem. Inf. Model., 2010)

Computational Study on the Interaction of N1 Substituted Pyrazole Derivatives with B-Raf Kinase: An Unusual Water Wire Hydrogen-Bond Network and Novel Interactions at the Entrance of the Active Site. - Jans H. Alzate-Morales; Ariela Vergara Jaque; Julio Caballero (J. Chem. Inf. Model., 2010)

Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2, 1-f][1, 2, 4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2, 3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine derivatives as c-Met kinase inhibitors. - Julio Caballero; Miguel Quiliano; Jans H. Alzate-Morales; Mirko Zimic; Eric Deharo (J. Comput. Aided Mol. Des., 2011)

Investigation of the Differences in Activity between Hydroxycycloalkyl N1 Substituted Pyrazole Derivatives As Inhibitors of B-Raf Kinase by Using Docking, Molecular Dynamics, QM/MM, and Fragment-Based De Novo Design: Study of Binding Mode of Diastereomer Compounds. - Julio Caballero; Jans H. Alzate-Morales; Ariela Vergara Jaque (J. Chem. Inf. Model., 2011)

In silico Comparison of Antimycobacterial Natural Products with Known Antituberculosis Drugs. - Marlene Espinoza-Moraga; Nicholas M. Njuguna; Grace Mugumbate; Julio Caballero; Kelly Chibale (J. Chem. Inf. Model., 2013)

The Dynamic Nonprime Binding of Sampatrilat to the C-Domain of Angiotensin-Converting Enzyme. - Rajni K. Sharma; Marlene Espinoza-Moraga; Horacio Poblete; Ross G. Douglas; Edward D. Sturrock; Julio Caballero; Kelly Chibale (J. Chem. Inf. Model., 2016)

Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors. - Julio Caballero; Alejandro Morales-Bayuelo; Carlos Navarro-Retamal (J. Comput. Aided Mol. Des., 2018)

Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide: Free energy perturbation (FEP) calculations. - Karel Mena-Ulecia; Fabián González-Norambuena; Ariela Vergara Jaque; Horacio Poblete; William Tiznado; Julio Caballero (J. Comput. Chem., 2018)

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)

Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins. - Erix Wiliam Hernández-Rodríguez; Andrés M. Escorcia; Marc van der Kamp; Ana Lilian Montero-Alejo; Julio Caballero (J. Comput. Chem., 2020)

BitClust: Fast Geometrical Clustering of Long Molecular Dynamics Simulations. - Roy González-Alemán; David Hernández-Castillo; Alejandro Rodríguez-Serradet; Julio Caballero; Erix Wiliam Hernández-Rodríguez; Luis Alberto Montero-Cabrera (J. Chem. Inf. Model., 2020)

Quality Threshold Clustering of Molecular Dynamics: A Word of Caution. - Roy González-Alemán; David Hernández-Castillo; Julio Caballero; Luis Alberto Montero-Cabrera (J. Chem. Inf. Model., 2020)

Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field. - Florencia Klein; Daniela Cáceres; Mónica A. Carrasco; Juan Carlos Tapia; Julio Caballero; Jans H. Alzate-Morales; Sergio Pantano (J. Chem. Inf. Model., 2020)

New Insights into the Opening of the Occluded Ligand-Binding Pocket of Sigma1 Receptor: Binding of a Novel Bivalent RC-33 Derivative. - Giacomo Rossino; Ivana Orellana; Julio Caballero; Dirk Schepmann; Bernhard Wünsch; Marta Rui; Daniela Rossi; Mariela González-Avendaño; Simona Collina; Ariela Vergara Jaque (J. Chem. Inf. Model., 2020)

BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics. - Roy González-Alemán; Daniel Platero-Rochart; David Hernández-Castillo; Erix Wiliam Hernández-Rodríguez; Julio Caballero; Fabrice Leclerc; Luis Alberto Montero-Cabrera (Bioinform., 2021)

PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations. - Francisco Adasme-Carreño; Julio Caballero; Joel Ireta (J. Chem. Inf. Model., 2021)

RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics. - Daniel Platero-Rochart; Roy González-Alemán; Erix Wiliam Hernández-Rodríguez; Fabrice Leclerc; Julio Caballero; Luis Alberto Montero-Cabrera (Bioinform., 2022)

MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics. - Roy González-Alemán; Daniel Platero-Rochart; Alejandro Rodríguez-Serradet; Erix Wiliam Hernández-Rodríguez; Julio Caballero; Fabrice Leclerc; Luis Alberto Montero-Cabrera (Bioinform., 2022)

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)