Molecular modelling study of changes induced by netropsin binding to nucleosome core particles. - Juan Jesús Pérez; J. Portugal (Nucleic Acids Res., 1990)

SCF-MO study of the polyglycine II structure. - Carlos Alemán; Juan Jesús Pérez (J. Comput. Aided Mol. Des., 1993)

Comparison of methods to estimate the free energy of solvation: Importance in the modulation of the affinity of 3-benzazepines for the D1receptor. - Ibon Alkorta; Hugo O. Villar; Juan Jesús Pérez (J. Comput. Chem., 1993)

A proposed bioactive conformation of Peptide T. - Nuria B. Centeno; Juan Jesús Pérez (J. Comput. Aided Mol. Des., 1998)

BUNDLE: A program for building the transmembrane domains of G-protein-coupled receptors. - Marta Filizola; Juan Jesús Pérez; Maria Cartenì-Farina (J. Comput. Aided Mol. Des., 1998)

Molecular modeling study of the differential ligand-receptor interaction at the µ, delta and kappa opioid receptors. - Marta Filizola; Maria Cartenì-Farina; Juan Jesús Pérez (J. Comput. Aided Mol. Des., 1999)

Molecular dynamics study of peptide segments of the BH3 domain of the proapoptotic proteins Bak, Bax, Bid and Hrk bound to the Bcl-xL and Bcl-2 proteins. - Marta Pinto; Juan Jesús Pérez; Jaime Rubio-Martinez (J. Comput. Aided Mol. Des., 2004)

Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics. - Francesc Corcho; Josep Cantó; Juan Jesús Pérez (J. Comput. Chem., 2004)

Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer. - Arnau Cordomí; Olle Edholm; Juan Jesús Pérez (J. Comput. Chem., 2007)

Complete maps of molecular-loop conformational spaces. - Josep M. Porta; Lluís Ros; Federico Thomas; Francesc Corcho; Josep Cantó; Juan Jesús Pérez (J. Comput. Chem., 2008)

Randomized tree construction algorithm to explore energy landscapes. - Leonard Jaillet; Francesc Corcho; Juan Jesús Pérez; Juan Cortés (J. Comput. Chem., 2011)

Rational Design of New Class of BH3-Mimetics As Inhibitors of the Bcl-xL Protein. - Marta Pinto; Maria del Mar Orzaez; Laura Delgado-Soler; Juan Jesús Pérez; Jaime Rubio-Martinez (J. Chem. Inf. Model., 2011)

New insights into the stereochemical requirements of the bradykinin B2 receptor antagonists binding. - Cecylia S. Lupala; Patricia Gómez-Gutiérrez; Juan Jesús Pérez (J. Comput. Aided Mol. Des., 2016)

Assessment of the Sampling Performance of Multiple-Copy Dynamics versus a Unique Trajectory. - Juan Jesús Pérez; Maria Santos Tomás; Jaime Rubio-Martinez (J. Chem. Inf. Model., 2016)

Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase. - Patricia Gómez-Gutiérrez; Jaime Rubio-Martinez; Juan Jesús Pérez (J. Chem. Inf. Model., 2017)

Molecular Determinants for the Activation/Inhibition of Bak Protein by BH3 Peptides. - Guillem Vila-Julià; José M. Granadino-Roldán; Juan Jesús Pérez; Jaime Rubio-Martinez (J. Chem. Inf. Model., 2020)

Discovery of Diverse Natural Products as Inhibitors of SARS-CoV-2 Mpro Protease through Virtual Screening. - Jaime Rubio-Martinez; Ana Jiménez-Alesanco; Laura Ceballos-Laita; David Ortega-Alarcón; Sonia Vega; Cristina Calvo; Cristina Benítez; Olga Abian; Adrián Velázquez-Campoy; Timothy M. Thomson; José Manuel Granadino-Roldán; Patricia Gómez-Gutiérrez; et al. (J. Chem. Inf. Model., 2021)

A Step Forward toward Selective Activation/Inhibition of Bak, a Pro-Apoptotic Member of the Bcl-2 Protein Family: Discovery of New Prospective Allosteric Sites Using Molecular Dynamics. - Guillem Vila-Julià; Juan Jesús Pérez; Jaime Rubio-Martinez (J. Chem. Inf. Model., 2023)

Discovery of Hit Compounds Targeting the P4 Allosteric Site of K-RAS, Identified through Ensemble-Based Virtual Screening. - Patricia Gómez-Gutiérrez; Jaime Rubio-Martinez; Juan Jesús Pérez (J. Chem. Inf. Model., 2023)

The Discovery of inhibitors of the SARS-CoV-2 S protein through computational drug repurposing. - Ana Isabel Avilés-Alía; Joao Zulaica; Juan Jesús Pérez; Jaime Rubio-Martinez; Ron Geller; José M. Granadino-Roldán (Comput. Biol. Medicine, 2024)