Julio Caballero

24 papers Journal 24
YearRankTypeTitle / Venue / Authors
2025 J jnl
CorrEA: A Web Server for Optimizing Correlations between Calculated Energies and Activities in Ligand-Receptor Systems Considering Multiple Binding Site Conformations.
J. Chem. Inf. Model.
Sergio Alfaro, Fabián González-Norambuena, José Luis Velázquez-Libera, Francisco Adasme-Carreño, Julio Caballero
2024 J jnl
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.
J. Chem. Inf. Model.
José Luis Velázquez-Libera, Julio Caballero, Jans H. Alzate-Morales, Jose Javier Ruiz-Pernía, Iñaki Tuñón
2022 J jnl
MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics.
Bioinform.
Roy González-Alemán, Daniel Platero-Rochart, Alejandro Rodríguez-Serradet, Erix Wiliam Hernández-Rodríguez, Julio Caballero, Fabrice Leclerc, Luis Alberto Montero-Cabrera
2022 J jnl
RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics.
Bioinform.
Daniel Platero-Rochart, Roy González-Alemán, Erix Wiliam Hernández-Rodríguez, Fabrice Leclerc, Julio Caballero, Luis Alberto Montero-Cabrera
2021 J jnl
BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics.
Bioinform.
Roy González-Alemán, Daniel Platero-Rochart, David Hernández-Castillo, Erix Wiliam Hernández-Rodríguez, Julio Caballero, Fabrice Leclerc, Luis Alberto Montero-Cabrera
2021 J jnl
PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations.
J. Chem. Inf. Model.
Francisco Adasme-Carreño, Julio Caballero, Joel Ireta
2020 J jnl
BitClust: Fast Geometrical Clustering of Long Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Roy González-Alemán, David Hernández-Castillo, Alejandro Rodríguez-Serradet, Julio Caballero, Erix Wiliam Hernández-Rodríguez, Luis Alberto Montero-Cabrera
2020 J jnl
Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field.
J. Chem. Inf. Model.
Florencia Klein, Daniela Cáceres, Mónica A. Carrasco, Juan Carlos Tapia, Julio Caballero, Jans H. Alzate-Morales, Sergio Pantano
2020 J jnl
LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking.
Bioinform.
José Luis Velázquez-Libera, Fabio Durán-Verdugo, Alejandro Valdés-Jiménez, Gabriel Núñez-Vivanco, Julio Caballero
2020 J jnl
Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins.
J. Comput. Chem.
Erix Wiliam Hernández-Rodríguez, Andrés M. Escorcia, Marc van der Kamp, Ana Lilian Montero-Alejo, Julio Caballero
2020 J jnl
New Insights into the Opening of the Occluded Ligand-Binding Pocket of Sigma1 Receptor: Binding of a Novel Bivalent RC-33 Derivative.
J. Chem. Inf. Model.
Giacomo Rossino, Ivana Orellana, Julio Caballero, Dirk Schepmann, Bernhard Wünsch, Marta Rui, Daniela Rossi, Mariela González-Avendaño, Simona Collina, Ariela Vergara Jaque
2020 J jnl
Quality Threshold Clustering of Molecular Dynamics: A Word of Caution.
J. Chem. Inf. Model.
Roy González-Alemán, David Hernández-Castillo, Julio Caballero, Luis Alberto Montero-Cabrera
2018 J jnl
Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors.
J. Comput. Aided Mol. Des.
Julio Caballero, Alejandro Morales-Bayuelo, Carlos Navarro-Retamal
2018 J jnl
Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide: Free energy perturbation (FEP) calculations.
J. Comput. Chem.
Karel Mena-Ulecia, Fabián González-Norambuena, Ariela Vergara Jaque, Horacio Poblete, William Tiznado, Julio Caballero
2016 J jnl
The Dynamic Nonprime Binding of Sampatrilat to the C-Domain of Angiotensin-Converting Enzyme.
J. Chem. Inf. Model.
Rajni K. Sharma, Marlene Espinoza-Moraga, Horacio Poblete, Ross G. Douglas, Edward D. Sturrock, Julio Caballero, Kelly Chibale
2013 J jnl
In silico Comparison of Antimycobacterial Natural Products with Known Antituberculosis Drugs.
J. Chem. Inf. Model.
Marlene Espinoza-Moraga, Nicholas M. Njuguna, Grace Mugumbate, Julio Caballero, Kelly Chibale
2011 J jnl
Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2, 1-
J. Comput. Aided Mol. Des.
Julio Caballero, Miguel Quiliano, Jans H. Alzate-Morales, Mirko Zimic, Eric Deharo
2011 J jnl
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
J. Chem. Inf. Model.
Julio Caballero, Jans H. Alzate-Morales, Ariela Vergara Jaque
2010 J jnl
Computational Study of the Interactions between Guanine Derivatives and Cyclin-Dependent Kinase 2 (CDK2) by CoMFA and QM/MM.
J. Chem. Inf. Model.
Jans H. Alzate-Morales, Julio Caballero
2010 J jnl
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.
J. Chem. Inf. Model.
Jans H. Alzate-Morales, Ariela Vergara Jaque, Julio Caballero
2009 J jnl
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.
J. Chem. Inf. Model.
Jans H. Alzate-Morales, Julio Caballero, Ariela Vergara Jaque, Fernando D. González Nilo
2006 J jnl
Amino Acid Sequence Autocorrelation Vectors and Ensembles of Bayesian-Regularized Genetic Neural Networks for Prediction of Conformational Stability of Human Lysozyme Mutants.
J. Chem. Inf. Model.
Julio Caballero, Leyden Fernández, José Ignacio Abreu, Michael Fernández
2005 J jnl
Genetic neural network modeling of the selective inhibition of the intermediate-conductance Ca
J. Comput. Aided Mol. Des.
Julio Caballero, Miguel Garriga, Michael Fernández
2005 J jnl
Modeling of Cyclin-Dependent Kinase Inhibition by 1
J. Chem. Inf. Model.
Michael Fernández, Alain Tundidor-Camba, Julio Caballero