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

TEFOOL/2: a program for theoretical drug design on microcomputers. - Modesto Orozco; Rafael Franco (Comput. Appl. Biosci., 1989)

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)

On the suitability of semiempirical calculations as sources of force field parameters. - Carlos Alemán; Modesto Orozco (J. Comput. Aided Mol. Des., 1992)

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)

Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges. - Heather A. Carlson; Toan B. Nguyen; Modesto Orozco; William L. Jorgensen (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)

Annotation of Non-Human Pathological Mutations utilising Human-Parameterised Neural Networks. - Carles Ferrer-Costa; Modesto Orozco; Xavier de la Cruz (Spanish Bioinformatics Conference, 2004)

Triplex-Forming Sequences in Regulatory Regions. - Josep Ramón Goñi; Modesto Orozco (Spanish Bioinformatics Conference, 2004)

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)

Comparative Study of MAPK 9 Alternative Splicing from Human and Mouse. - David Talavera; Carles Ferrer-Costa; Modesto Orozco; Xavier de la Cruz (Spanish Bioinformatics Conference, 2004)

Comparison of Active Centers of Proteins: The Kinesin Family as a Test Case. - Antoni Valencia; Martín Pérez; Adam Hospital; Joan Carles Fernández; Elena Manresa; Robert Soliva; Josep Lluis Gelpí; Modesto Orozco (Spanish Bioinformatics Conference, 2004)

PMUT: a web-based tool for the annotation of pathological mutations on proteins. - Carles Ferrer-Costa; Josep Lluis Gelpí; Leire Zamakola; Ivan Parraga; Xavier de la Cruz; Modesto Orozco (Bioinform., 2005)

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)

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. - Lucía Conde; Juan M. Vaquerizas; Carles Ferrer-Costa; Xavier de la Cruz; Modesto Orozco; Joaquín Dopazo (Nucleic Acids Res., 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)

A procedure for identifying homologous alternative splicing events. - David Talavera; Adam Hospital; Modesto Orozco; Xavier de la Cruz (BMC Bioinform., 2007)

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)

The (In)dependence of Alternative Splicing and Gene Duplication. - David Talavera; Christine Vogel; Modesto Orozco; Sarah A. Teichmann; Xavier de la Cruz (PLoS Comput. Biol., 2007)

A consensus view of protein dynamics. - Manuel Rueda; Carles Ferrer-Costa; Tim Meyer; Alberto Pérez; Jordi Camps; Adam Hospital; Josep Lluis Gelpí; Modesto Orozco (Proc. Natl. Acad. Sci. USA, 2007)

DNAlive: a tool for the physical analysis of DNA at the genomic scale. - Josep Ramón Goñi; Carlos Fenollosa; Alberto Pérez; David Torrents; Modesto Orozco (Bioinform., 2008)

FlexServ: an integrated tool for the analysis of protein flexibility. - Jordi Camps; Oliver Carrillo; Agustí Emperador; Laura Orellana; Adam Hospital; Manuel Rueda; Damjan Cicin-Sain; Marco D'Abramo; Josep Lluis Gelpí; Modesto Orozco (Bioinform., 2009)

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)

nucleR: a package for non-parametric nucleosome positioning. - Oscar Flores; Modesto Orozco (Bioinform., 2011)

Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking. - Carles Pons; David Talavera; Xavier de la Cruz; Modesto Orozco; Juan Fernández-Recio (J. Chem. Inf. Model., 2011)

Nucleotide Binding Switches the Information Flow in Ras GTPases. - Francesco Raimondi 001; Guillem Portella; Modesto Orozco; Francesca Fanelli (PLoS Comput. Biol., 2011)

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. - Adam Hospital; Pau Andrio; Carlos Fenollosa; Damjan Cicin-Sain; Modesto Orozco; Josep Lluis Gelpí (Bioinform., 2012)

Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case. - Rebeca García-Fandiño; Pau Bernadó; Sara Ayuso-Tejedor; Javier Sancho; Modesto Orozco (PLoS Comput. Biol., 2012)

Exploration of conformational transition pathways from coarse-grained simulations. - Pedro Sfriso; Adam Hospital; Agustí Emperador; Modesto Orozco (Bioinform., 2013)

NAFlex: a web server for the study of nucleic acid flexibility. - Adam Hospital; Ignacio Faustino; Rosana Collepardo-Guevara; Carlos González; Josep Lluis Gelpí; Modesto Orozco (Nucleic Acids Res., 2013)

Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale. - Michela Candotti; Alberto Pérez; Carles Ferrer-Costa; Manuel Rueda; Tim Meyer; Josep Lluis Gelpí; Modesto Orozco (PLoS Comput. Biol., 2013)

Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations. - Guillem Portella; Federica Battistini; Modesto Orozco (PLoS Comput. Biol., 2013)

SEABED: Small molEcule activity scanner weB servicE baseD. - Carlos Fenollosa; Marcel Otón; Pau Andrio; Jorge Cortés 002; Modesto Orozco; Josep Ramón Goñi (Bioinform., 2015)

Computational Prediction of HIV-1 Resistance to Protease Inhibitors. - Ali Hosseini; Andreu Alibés; Marc Noguera-Julian; Víctor A. Gil; Roger Paredes; Robert Soliva; Modesto Orozco; Victor Guallar (J. Chem. Inf. Model., 2016)

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. - Adam Hospital; Pau Andrio; Cesare Cugnasco; Laia Codó; Yolanda Becerra 001; Pablo D. Dans; Federica Battistini; Jordi Torres; Josep Ramón Goñi; Modesto Orozco; Josep Lluis Gelpí (Nucleic Acids Res., 2016)

The Differential Response of Proteins to Macromolecular Crowding. - Michela Candotti; Modesto Orozco (PLoS Comput. Biol., 2016)

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data. - Ardita Shkurti; Josep Ramón Goñi; Pau Andrio; Elena Breitmoser; Iain Bethune; Modesto Orozco; Charles A. Laughton (SoftwareX, 2016)

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. - Víctor López-Ferrando; Andrea M. Gazzo; Xavier de la Cruz; Modesto Orozco; Josep Lluis Gelpí (Nucleic Acids Res., 2017)

Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs. - Martin Kotev; Pilar Manuel-Manresa; Elsa Hernando; Vanessa Soto-Cerrato; Modesto Orozco; Roberto Quesada; Ricardo Pérez-Tomás; Victor Guallar (J. Chem. Inf. Model., 2017)

VeriNA3d: an R package for nucleic acids data mining. - Diego Gallego; Leonardo Darré; Pablo D. Dans; Modesto Orozco (Bioinform., 2019)

Molywood: streamlining the design and rendering of molecular movies. - Milosz Wieczór; Adam Hospital; Genís Bayarri; Jacek Czub; Modesto Orozco (Bioinform., 2020)

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function. - Federica Battistini; Pablo D. Dans; Montserrat Terrazas; Chiara L. Castellazzi; Guillem Portella; Mireia Labrador; Núria Villegas; Isabelle Brun-Heath; Carlos González; Modesto Orozco (PLoS Comput. Biol., 2021)

BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools. - Genís Bayarri; Pau Andrio; Adam Hospital; Modesto Orozco; Josep Lluis Gelpí (Bioinform., 2022)

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. - Genís Bayarri; Pau Andrio; Adam Hospital; Modesto Orozco; Josep Lluis Gelpí (Nucleic Acids Res., 2022)

Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation. - Benjamin Martin; Pablo D. Dans; Milosz Wieczór; Núria Villegas; Isabelle Brun-Heath; Federica Battistini; Montserrat Terrazas; Modesto Orozco (PLoS Comput. Biol., 2022)

High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations. - Aristarc Suriñach; Adam Hospital; Yvonne Westermaier; Luis Jordà; Sergi Orozco-Ruiz; Daniel Beltrán; Francesco Colizzi; Pau Andrio; Robert Soliva; Martí Municoy; Josep Lluis Gelpí; Modesto Orozco (J. Chem. Inf. Model., 2023)

Sequence-Dependent Properties of the RNA Duplex. - Federica Battistini; Alba Sala; Adam Hospital; Modesto Orozco (J. Chem. Inf. Model., 2023)

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows. - Genís Bayarri; Pau Andrio; Josep Lluis Gelpí; Adam Hospital; Modesto Orozco (PLoS Comput. Biol., 2024)

Gromologist: A GROMACS-oriented utility library for structure and topology manipulation. - Milosz Wieczór; Jacek Czub; Modesto Orozco (SoftwareX, 2025)