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 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)

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)

Molecular Basis of Drug Resistance in A/H1N1 Virus. - Ariela Vergara Jaque; Horacio Poblete; Eric H. Lee; Klaus Schulten; Fernando D. González Nilo; Christophe Chipot (J. Chem. Inf. Model., 2012)

Iodide Binding in Sodium-Coupled Cotransporters. - Ariela Vergara Jaque; Peying Fong; Jeffrey Comer (J. Chem. Inf. Model., 2017)

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)

Structural Determinants of the Dopamine Transporter Regulation Mediated by G Proteins. - Genoveva Rojas; Ivana Orellana; Roberto Rosales-Rojas; Jennie García-Olivares; Jeffrey Comer; Ariela Vergara Jaque (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)

Structural Insights into the Inhibition Site in the Phosphorylcholine Phosphatase Enzyme of Pseudomonas aeruginosa. - Daniel Bustos; Erix Wiliam Hernández-Rodríguez; Horacio Poblete; Jans H. Alzate-Morales; Cecilia Challier; Cristhian Boetsch; Ariela Vergara Jaque; Paola Beassoni (J. Chem. Inf. Model., 2022)

Understanding the Differences of Danusertib's Residence Time in Aurora Kinases A/B: Dissociation Paths and Key Residues Identified using Conventional and Enhanced Molecular Dynamics Simulations. - Felipe Bravo-Moraga; Mauricio Bedoya; Ariela Vergara Jaque; Jans H. Alzate-Morales (J. Chem. Inf. Model., 2024)