POEMS: program for outliers elimination in multidimensional space. - Modesto Orozco; F. Javier Luque (Comput. Appl. Biosci., 1988)

POEAMS: program for outliers elimination in 'anomalous' multidimensional space. - Modesto Orozco; F. Javier Luque (Comput. Appl. Biosci., 1989)

A practical procedure for the determination of electrostatic charges of large molecules. - Modesto Orozco; F. Javier Luque (J. Comput. Aided Mol. Des., 1990)

A new scaling procedure to correct semiempirical MEP and MEP-derived properties. - Carlos Alemán; F. Javier Luque; Modesto Orozco (J. Comput. Aided Mol. Des., 1993)

Suitability of the PM3-derived molecular electrostatic potentials. - Carlos Alemán; F. Javier Luque; Modesto Orozco (J. Comput. Chem., 1993)

Comparison of 6-31G*-based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules. - Modesto Orozco; William L. Jorgensen; F. Javier Luque (J. Comput. Chem., 1993)

Molecular interaction potential: A new tool for the theoretical study of molecular reactivity. - Modesto Orozco; F. Javier Luque (J. Comput. Chem., 1993)

Ab initio study of bond stretching: Implications in force-field parametrization for molecular mechanics and dynamics. - Modesto Orozco; F. Javier Luque (J. Comput. Chem., 1993)

Comparison of NDDO and Quasi-Ab Initio Approaches to Compute Semiempirical Molecular Electrostatic Potentials. - Cristóbal Alhambra; Francisco Javier Luque; Modesto Orozco (J. Comput. Chem., 1994)

Optimization of Solute Cavities and van der Waals Parameters in Ab Initio MST-SCRF Calculations of Neutral Molecules. - Margarida Bachs; F. Javier Luque; Modesto Orozco (J. Comput. Chem., 1994)

An Optimized AM1/MST Method for the MST-SCRF Representation of Solvated Systems. - F. Javier Luque; Margarida Bachs; Modesto Orozco (J. Comput. Chem., 1994)

Development of Optimized MST/SCRF Methods for Semiempirical Calculations: The MNDO and PM3 Hamilitonians. - Modesto Orozco; Margarida Bachs; F. Javier Luque (J. Comput. Chem., 1995)

Tautomerism of xanthine and alloxanthine: A model for substrate recognition by xanthine oxidase. - Begoña Hernández; Modesto Orozco; F. Javier Luque (J. Comput. Aided Mol. Des., 1996)

Extension of MST/SCRF method to organic solvents: Ab initio and semiempirical parametrization for neutral solutes in CCl4. - F. Javier Luque; Margarida Bachs; Carlos Alemán; Modesto Orozco (J. Comput. Chem., 1996)

Role of the tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase. - Begoña Hernández; Modesto Orozco; F. Javier Luque (J. Comput. Aided Mol. Des., 1997)

Suitability of density functional methods for calculation of electrostatic properties. - Robert Soliva; Modesto Orozco; F. Javier Luque (J. Comput. Chem., 1997)

Polarization effects in generalized molecular interaction potential: New Hamiltonian for reactivity studies and mixed QM/MM calculations. - F. Javier Luque; Modesto Orozco (J. Comput. Chem., 1998)

Fractional description of free energies of solvation. - F. Javier Luque; Xavier Barril; Modesto Orozco (J. Comput. Aided Mol. Des., 1999)

Monte Carlo-MST: New strategy for representation of solvent configurational space in solution. - Carles Colominas; F. Javier Luque; Modesto Orozco (J. Comput. Chem., 1999)

Parametrization of the GMIPp for the study of stacking interactions. - Begoña Hernández; F. Javier Luque; Modesto Orozco (J. Comput. Chem., 1999)

Mixed QM/MM molecular electrostatic potentials. - Begoña Hernández; F. Javier Luque; Modesto Orozco (J. Comput. Aided Mol. Des., 2000)

Solvation in octanol: parametrization of the continuum MST model. - Carles Curutchet; Modesto Orozco; F. Javier Luque (J. Comput. Chem., 2001)

Ligand-induced changes in the binding sites of proteins. - Xavier Fradera; Xavier de la Cruz; Carlos H. Tomich P. Silva; Josep Lluis Gelpí; F. Javier Luque; Modesto Orozco (Bioinform., 2002)

Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study. - Albert Salichs; M. López; V. Segarra; Modesto Orozco; F. Javier Luque (J. Comput. Aided Mol. Des., 2002)

Hydrophobic similarity between molecules: A MST-based hydrophobic similarity index. - Jordi Muñoz; Xavier Barril; Begoña Hernández; Modesto Orozco; F. Javier Luque (J. Comput. Chem., 2002)

Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations. - Carles Curutchet; Josep Maria Bofill; Begoña Hernández; Modesto Orozco; F. Javier Luque (J. Comput. Chem., 2003)

Electrostatic component of solvation: Comparison of SCRF continuum models. - Carles Curutchet; Christopher J. Cramer; Donald G. Truhlar; Manuel F. Ruiz-López; Daniel Rinaldi; Modesto Orozco; F. Javier Luque (J. Comput. Chem., 2003)

Transferability of fragmental contributions to the octanol/water partition coefficient: An NDDO-based MST study. - Carles Curutchet; Albert Salichs; Xavier Barril; Modesto Orozco; Francisco Javier Luque (J. Comput. Chem., 2003)

Continuum and discrete calculation of fractional contributions to solvation free energy. - Antonio Morreale; Josep Lluis Gelpí; F. Javier Luque; Modesto Orozco (J. Comput. Chem., 2003)

Hydration Free Energy in Macromolecules. - Antonio Morreale; Xavier de la Cruz; Tim Meyer; Josep Lluis Gelpí; F. Javier Luque; Modesto Orozco (Spanish Bioinformatics Conference, 2004)

Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient. - Jordi Muñoz-Muriedas; Samantha Perspicace; Nuria Bech; Salvatore Guccione; Modesto Orozco; F. Javier Luque (J. Comput. Aided Mol. Des., 2005)

Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model. - Carles Curutchet; Modesto Orozco; F. Javier Luque; Benedetta Mennucci; Jacopo Tomasi (J. Comput. Chem., 2006)

Extension of the MST continuum solvation model to the RM1 semiempirical hamiltonian. - Flavio Forti; Xavier Barril; F. Javier Luque; Modesto Orozco (J. Comput. Chem., 2007)

Toward accurate relative energy predictions of the bioactive conformation of drugs. - Keith T. Butler; F. Javier Luque; Xavier Barril (J. Comput. Chem., 2009)

Virtual Domotic Systems: a 3D interaction technique to control virtual building devices using residential gateways. - Francisco Pedro Luque; Francisco Javier Luque; Carmen Lastres; Asunción Santamaria; Iris Galloso; J. Muria (IPTA, 2010)

Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar. - Constanza Cárdenas; Axel Bidon-Chanal; Pablo Conejeros; Gloria Arenas; Sergio Marshall; F. Javier Luque (J. Comput. Aided Mol. Des., 2010)

Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. - Ignacio Soteras; Modesto Orozco; F. Javier Luque (J. Comput. Aided Mol. Des., 2010)

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories. - Peter Schmidtke; Axel Bidon-Chanal; F. Javier Luque; Xavier Barril (Bioinform., 2011)

Molecular simulation methods in drug discovery: a prospective outlook. - Xavier Barril; F. Javier Luque (J. Comput. Aided Mol. Des., 2012)

TuberQ: a Mycobacterium tuberculosis protein druggability database. - Leandro G. Radusky; Lucas A. Defelipe; Esteban Lanzarotti; F. Javier Luque; Xavier Barril; Marcelo A. Marti; Adrian Gustavo Turjanski (Database J. Biol. Databases Curation, 2014)

Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields. - Marie Zgarbová; Andreana M. Rosnik; F. Javier Luque; Carles Curutchet; Petr Jurecka (J. Comput. Chem., 2015)

Methodology for Evaluating the Quality of Ecosystem Maps: A Case Study in the Andes. - Dolors Armenteras; Tania Marisol González; Francisco Javier Luque; Denis López; Nelly Rodríguez (ISPRS Int. J. Geo Inf., 2016)

Development and validation of hydrophobic molecular fields derived from the quantum mechanical IEF/PCM-MST solvation models in 3D-QSAR. - Tiziana Ginex; Jordi Muñoz-Muriedas; Enric Herrero; Enric Gibert; Pietro Cozzini; F. Javier Luque (J. Comput. Chem., 2016)

Development and Validation of Molecular Overlays Derived from Three-Dimensional Hydrophobic Similarity with PharmScreen. - Javier Vázquez; Alessandro Deplano; Albert Herrero; Tiziana Ginex; Enric Gibert; Obdulia Rabal; Julen Oyarzabal; Enric Herrero; F. Javier Luque (J. Chem. Inf. Model., 2018)

Understanding the Mechanism of Direct Activation of AMP-Kinase: Toward a Fine Allosteric Tuning of the Kinase Activity. - Elnaz Aledavood; Gleiciane Moraes; Jerônimo Lameira; Ana Castro; F. Javier Luque; Carolina Estarellas (J. Chem. Inf. Model., 2019)

Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations. - Laia Julió Plana; Alejandro D. Nadra; Dario A. Estrin; F. Javier Luque; Luciana Capece (J. Chem. Inf. Model., 2019)

Prediction of the n-octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations. - William J. Zamora; Silvana Pinheiro; Kilian German; Clara Pérez-Ràfols; Carles Curutchet; F. Javier Luque (J. Comput. Aided Mol. Des., 2020)

Assessing the Performance of Mixed Strategies To Combine Lipophilic Molecular Similarity and Docking in Virtual Screening. - Javier Vázquez; Alessandro Deplano; Albert Herrero; Enric Gibert; Enric Herrero; F. Javier Luque (J. Chem. Inf. Model., 2020)

Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model. - Antonio Viayna; Silvana Pinheiro; Carles Curutchet; F. Javier Luque; William J. Zamora (J. Comput. Aided Mol. Des., 2021)

Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations. - Vinícius Bonatto; Anwar Shamim; Fernanda dos R. Rocho; Andrei Leitão; F. Javier Luque; Jerônimo Lameira; Carlos Alberto Montanari (J. Chem. Inf. Model., 2021)

Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits. - Javier Vázquez; Tiziana Ginex; Albert Herrero; Christophe Morisseau; Bruce D. Hammock; F. Javier Luque (J. Chem. Inf. Model., 2023)

Binding of Cholesterol to the N-Terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerization-Related Binding Selectivity and Loop Mutations. - Aitor Valdivia; F. Javier Luque; Salomé Llabrés (J. Chem. Inf. Model., 2024)

On the relevance of query definition in the performance of 3D ligand-based virtual screening. - Javier Vázquez; Ricardo García; Paula Llinares; F. Javier Luque; Enric Herrero (J. Comput. Aided Mol. Des., 2024)

Extending the MST Model to Large Biomolecular Systems: Parametrization of the ddCOSMO-MST Continuum Solvation Model. - Renato D. Cunha; S. Romero-Téllez; Filippo Lipparini; F. Javier Luque; Carles Curutchet (J. Comput. Chem., 2025)

Synthon-Based Strategies Exploiting Molecular Similarity and Protein-Ligand Interactions for Efficient Screening of Ultra-Large Chemical Libraries. - Brian Medel-Lacruz; Albert Herrero; Fernando Martín; Enric Herrero; F. Javier Luque; Javier Vázquez (J. Chem. Inf. Model., 2025)