Modesto Orozco

Publication Activity (10 Years)

Years Active: 1988-2023
Publications (10 Years): 14

Top Topics

Simulation Tools

Top Venues

PLoS Comput. Biol.

J. Chem. Inf. Model.

Nucleic Acids Res.

Publications

Federica Battistini, Alba Sala, Adam Hospital, Modesto Orozco
Sequence-Dependent Properties of the RNA Duplex. J. Chem. Inf. Model. 63 (16) (2023)
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
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. J. Chem. Inf. Model. 63 (1) (2023)
Genis Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluis Gelpí
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. Nucleic Acids Res. 50 (W1) (2022)
Genis Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluis Gelpí
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools. Bioinform. 38 (12) (2022)
Benjamin Martin, Pablo D. Dans, Milosz Wieczór, Núria Villegas, Isabelle Brun-Heath, Federica Battistini, Montserrat Terrazas, Modesto Orozco
Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation. PLoS Comput. Biol. 18 (1) (2022)
Federica Battistini, Pablo D. Dans, Montserrat Terrazas, Chiara L. Castellazzi, Guillem Portella, Mireia Labrador, Núria Villegas, Isabelle Brun-Heath, Carlos González, Modesto Orozco
The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function. PLoS Comput. Biol. 17 (11) (2021)
Milosz Wieczór, Adam Hospital, Genis Bayarri, Jacek Czub, Modesto Orozco
Molywood: streamlining the design and rendering of molecular movies. Bioinform. 36 (17) (2020)
Diego Gallego, Leonardo Darré, Pablo D. Dans, Modesto Orozco
VeriNA3d: an R package for nucleic acids data mining. Bioinform. 35 (24) (2019)
Víctor López-Ferrando, Andrea M. Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Lluis Gelpí
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Martin Kotev, Pilar Manuel-Manresa, Elsa Hernando, Vanessa Soto-Cerrato, Modesto Orozco, Roberto Quesada, Ricardo Pérez-Tomás, Victor Guallar
Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs. J. Chem. Inf. Model. 57 (8) (2017)
Ali Hosseini, Andreu Alibés, Marc Noguera-Julian, Víctor A. Gil, Roger Paredes, Robert Soliva, Modesto Orozco, Victor Guallar
Computational Prediction of HIV-1 Resistance to Protease Inhibitors. J. Chem. Inf. Model. 56 (5) (2016)
Ardita Shkurti, Josep Ramón Goñi, Pau Andrio, Elena Breitmoser, Iain Bethune, Modesto Orozco, Charles A. Laughton
pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data. SoftwareX 5 (2016)
Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codó, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Josep Ramón Goñi, Modesto Orozco, Josep Lluis Gelpí
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. Nucleic Acids Res. 44 (Database-Issue) (2016)
Michela Candotti, Modesto Orozco
The Differential Response of Proteins to Macromolecular Crowding. PLoS Comput. Biol. 12 (7) (2016)
Carlos Fenollosa, Marcel Otón, Pau Andrio, Jorge Cortés, Modesto Orozco, Josep Ramón Goñi
SEABED: Small molEcule activity scanner weB servicE baseD. Bioinform. 31 (5) (2015)
Guillem Portella, Federica Battistini, Modesto Orozco
Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations. PLoS Comput. Biol. 9 (11) (2013)
Adam Hospital, Ignacio Faustino, Rosana Collepardo-Guevara, Carlos González, Josep Lluis Gelpí, Modesto Orozco
NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Pedro Sfriso, Adam Hospital, Agustí Emperador, Modesto Orozco
Exploration of conformational transition pathways from coarse-grained simulations. Bioinform. 29 (16) (2013)
Michela Candotti, Alberto Pérez, Carles Ferrer-Costa, Manuel Rueda, Tim Meyer, Josep Lluis Gelpí, Modesto Orozco
Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale. PLoS Comput. Biol. 9 (12) (2013)
Adam Hospital, Pau Andrio, Carlos Fenollosa, Damjan Cicin-Sain, Modesto Orozco, Josep Lluis Gelpí
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinform. 28 (9) (2012)
Rebeca García-Fandiño, Pau Bernadó, Sara Ayuso-Tejedor, Javier Sancho, Modesto Orozco
Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case. PLoS Comput. Biol. 8 (8) (2012)
Francesco Raimondi, Guillem Portella, Modesto Orozco, Francesca Fanelli
Nucleotide Binding Switches the Information Flow in Ras GTPases. PLoS Comput. Biol. 7 (3) (2011)
Carles Pons, David Talavera, Xavier de la Cruz, Modesto Orozco, Juan Fernández-Recio
Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking. J. Chem. Inf. Model. 51 (2) (2011)
Oscar Flores, Modesto Orozco
nucleR: a package for non-parametric nucleosome positioning. Bioinform. 27 (15) (2011)
Ignacio Soteras, Modesto Orozco, F. Javier Luque
Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. J. Comput. Aided Mol. Des. 24 (4) (2010)
Jordi Camps, Oliver Carrillo, Agustí Emperador, Laura Orellana, Adam Hospital, Manuel Rueda, Damjan Cicin-Sain, Marco D'Abramo, Josep Lluis Gelpí, Modesto Orozco
FlexServ: an integrated tool for the analysis of protein flexibility. Bioinform. 25 (13) (2009)
Josep Ramón Goñi, Carlos Fenollosa, Alberto Pérez, David Torrents, Modesto Orozco
DNAlive: a tool for the physical analysis of DNA at the genomic scale. Bioinform. 24 (15) (2008)
David Talavera, Christine Vogel, Modesto Orozco, Sarah A. Teichmann, Xavier de la Cruz
The (In)dependence of Alternative Splicing and Gene Duplication. PLoS Comput. Biol. 3 (3) (2007)
David Talavera, Adam Hospital, Modesto Orozco, Xavier de la Cruz
A procedure for identifying homologous alternative splicing events. BMC Bioinform. 8 (2007)
Flavio Forti, Xavier Barril, F. Javier Luque, Modesto Orozco
Extension of the MST continuum solvation model to the RM1 semiempirical hamiltonian. J. Comput. Chem. 29 (4) (2007)
Manuel Rueda, Carles Ferrer-Costa, Tim Meyer, Alberto Pérez, Jordi Camps, Adam Hospital, Josep Lluis Gelpí, Modesto Orozco
A consensus view of protein dynamics. Proc. Natl. Acad. Sci. USA 104 (3) (2007)
Carles Curutchet, Modesto Orozco, F. Javier Luque, Benedetta Mennucci, Jacopo Tomasi
Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model. J. Comput. Chem. 27 (15) (2006)
Jordi Muñoz-Muriedas, Samantha Perspicace, Nuria Bech, Salvatore Guccione, Modesto Orozco, F. Javier Luque
Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient. J. Comput. Aided Mol. Des. 19 (6) (2005)
Lucía Conde, Juan M. Vaquerizas, Carles Ferrer-Costa, Xavier de la Cruz, Modesto Orozco, Joaquín Dopazo
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Carles Ferrer-Costa, Josep Lluis Gelpí, Leire Zamakola, Ivan Parraga, Xavier de la Cruz, Modesto Orozco
PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinform. 21 (14) (2005)
David Talavera, Carles Ferrer-Costa, Modesto Orozco, Xavier de la Cruz
Comparative Study of MAPK 9 Alternative Splicing from Human and Mouse. Spanish Bioinformatics Conference (2004)
Josep Ramón Goñi, Modesto Orozco
Triplex-Forming Sequences in Regulatory Regions. Spanish Bioinformatics Conference (2004)
Carles Ferrer-Costa, Modesto Orozco, Xavier de la Cruz
Annotation of Non-Human Pathological Mutations utilising Human-Parameterised Neural Networks. Spanish Bioinformatics Conference (2004)
Antoni Valencia, Martín Pérez, Adam Hospital, Joan Carles Fernández, Elena Manresa, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco
Comparison of Active Centers of Proteins: The Kinesin Family as a Test Case. Spanish Bioinformatics Conference (2004)
Antonio Morreale, Xavier de la Cruz, Tim Meyer, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco
Hydration Free Energy in Macromolecules. Spanish Bioinformatics Conference (2004)
Antonio Morreale, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco
Continuum and discrete calculation of fractional contributions to solvation free energy. J. Comput. Chem. 24 (13) (2003)
Carles Curutchet, Christopher J. Cramer, Donald G. Truhlar, Manuel F. Ruiz-López, Daniel Rinaldi, Modesto Orozco, F. Javier Luque
Electrostatic component of solvation: Comparison of SCRF continuum models. J. Comput. Chem. 24 (3) (2003)
Carles Curutchet, Albert Salichs, Xavier Barril, Modesto Orozco, Francisco Javier Luque
Transferability of fragmental contributions to the octanol/water partition coefficient: An NDDO-based MST study. J. Comput. Chem. 24 (1) (2003)
Carles Curutchet, Josep Maria Bofill, Begoña Hernández, Modesto Orozco, F. Javier Luque
Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations. J. Comput. Chem. 24 (10) (2003)
Jordi Muñoz, Xavier Barril, Begoña Hernández, Modesto Orozco, F. Javier Luque
Hydrophobic similarity between molecules: A MST-based hydrophobic similarity index. J. Comput. Chem. 23 (5) (2002)
Albert Salichs, M. López, V. Segarra, Modesto Orozco, F. Javier Luque
Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study. J. Comput. Aided Mol. Des. 16 (8-9) (2002)
Xavier Fradera, Xavier de la Cruz, Carlos H. Tomich P. Silva, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco
Ligand-induced changes in the binding sites of proteins. Bioinform. 18 (7) (2002)
Carles Curutchet, Modesto Orozco, F. Javier Luque
Solvation in octanol: parametrization of the continuum MST model. J. Comput. Chem. 22 (11) (2001)
Begoña Hernández, F. Javier Luque, Modesto Orozco
Mixed QM/MM molecular electrostatic potentials. J. Comput. Aided Mol. Des. 14 (4) (2000)
F. Javier Luque, Xavier Barril, Modesto Orozco
Fractional description of free energies of solvation. J. Comput. Aided Mol. Des. 13 (2) (1999)
Begoña Hernández, F. Javier Luque, Modesto Orozco
Parametrization of the GMIPp for the study of stacking interactions. J. Comput. Chem. 20 (9) (1999)
Carles Colominas, F. Javier Luque, Modesto Orozco
Monte Carlo-MST: New strategy for representation of solvent configurational space in solution. J. Comput. Chem. 20 (7) (1999)
F. Javier Luque, Modesto Orozco
Polarization effects in generalized molecular interaction potential: New Hamiltonian for reactivity studies and mixed QM/MM calculations. J. Comput. Chem. 19 (8) (1998)
Begoña Hernández, Modesto Orozco, F. Javier Luque
Role of the tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase. J. Comput. Aided Mol. Des. 11 (2) (1997)
Robert Soliva, Modesto Orozco, F. Javier Luque
Suitability of density functional methods for calculation of electrostatic properties. J. Comput. Chem. 18 (8) (1997)
Begoña Hernández, Modesto Orozco, F. Javier Luque
Tautomerism of xanthine and alloxanthine: A model for substrate recognition by xanthine oxidase. J. Comput. Aided Mol. Des. 10 (6) (1996)
F. Javier Luque, Margarida Bachs, Carlos Alemán, Modesto Orozco
Extension of MST/SCRF method to organic solvents: Ab initio and semiempirical parametrization for neutral solutes in CCl4. J. Comput. Chem. 17 (7) (1996)
Modesto Orozco, Margarida Bachs, F. Javier Luque
Development of Optimized MST/SCRF Methods for Semiempirical Calculations: The MNDO and PM3 Hamilitonians. J. Comput. Chem. 16 (5) (1995)
Margarida Bachs, F. Javier Luque, Modesto Orozco
Optimization of Solute Cavities and van der Waals Parameters in Ab Initio MST-SCRF Calculations of Neutral Molecules. J. Comput. Chem. 15 (4) (1994)
F. Javier Luque, Margarida Bachs, Modesto Orozco
An Optimized AM1/MST Method for the MST-SCRF Representation of Solvated Systems. J. Comput. Chem. 15 (8) (1994)
Cristóbal Alhambra, Francisco Javier Luque, Modesto Orozco
Comparison of NDDO and Quasi-Ab Initio Approaches to Compute Semiempirical Molecular Electrostatic Potentials. J. Comput. Chem. 15 (1) (1994)
Heather A. Carlson, Toan B. Nguyen, Modesto Orozco, William L. Jorgensen
Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges. J. Comput. Chem. 14 (10) (1993)
Carlos Alemán, F. Javier Luque, Modesto Orozco
A new scaling procedure to correct semiempirical MEP and MEP-derived properties. J. Comput. Aided Mol. Des. 7 (6) (1993)
Modesto Orozco, F. Javier Luque
Molecular interaction potential: A new tool for the theoretical study of molecular reactivity. J. Comput. Chem. 14 (5) (1993)
Modesto Orozco, William L. Jorgensen, F. Javier Luque
Comparison of 6-31G*-based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules. J. Comput. Chem. 14 (12) (1993)
Carlos Alemán, F. Javier Luque, Modesto Orozco
Suitability of the PM3-derived molecular electrostatic potentials. J. Comput. Chem. 14 (7) (1993)
Modesto Orozco, F. Javier Luque
study of bond stretching: Implications in force-field parametrization for molecular mechanics and dynamics. J. Comput. Chem. 14 (8) (1993)
Carlos Alemán, Modesto Orozco
On the suitability of semiempirical calculations as sources of force field parameters. J. Comput. Aided Mol. Des. 6 (4) (1992)
Modesto Orozco, F. Javier Luque
A practical procedure for the determination of electrostatic charges of large molecules. J. Comput. Aided Mol. Des. 4 (4) (1990)
Modesto Orozco, F. Javier Luque
POEAMS: program for outliers elimination in 'anomalous' multidimensional space. Comput. Appl. Biosci. 5 (3) (1989)
Modesto Orozco, Rafael Franco
TEFOOL/2: a program for theoretical drug design on microcomputers. Comput. Appl. Biosci. 5 (3) (1989)
Modesto Orozco, F. Javier Luque
POEMS: program for outliers elimination in multidimensional space. Comput. Appl. Biosci. 4 (3) (1988)