Modesto Orozco

74 papers Journal 69Unranked 5

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	When the Position of Pendant Groups Makes the Difference in G-Quadruplex Behavior: The Case of Bis-Conjugated Thrombin-Binding Aptamers. J. Chem. Inf. Model. Chiara Platella, Federica Battistini, Claudia Riccardi, Michael Smietana, François Morvan, Modesto Orozco, Daniela Montesarchio
2025	J	`jnl`	Gromologist: A GROMACS-oriented utility library for structure and topology manipulation. SoftwareX Milosz Wieczór, Jacek Czub, Modesto Orozco
2024	J	`jnl`	Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows. PLoS Comput. Biol. Genís Bayarri, Pau Andrio, Josep Lluís Gelpí, Adam Hospital, Modesto Orozco
2023	J	`jnl`	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. Aristarc Suriñach, Adam Hospital, Yvonne Westermaier, Luis Jordà, Sergi Orozco-Ruiz, Daniel Beltrán, Francesco Colizzi, Pau Andrio, Robert Soliva, Martí Municoy, Josep Lluís Gelpí, Modesto Orozco
2023	J	`jnl`	Sequence-Dependent Properties of the RNA Duplex. J. Chem. Inf. Model. Federica Battistini, Alba Sala, Adam Hospital, Modesto Orozco
2022	J	`jnl`	BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools. Bioinform. Genís Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluís Gelpí
2022	J	`jnl`	BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. Nucleic Acids Res. Genís Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluís Gelpí
2022	J	`jnl`	Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation. PLoS Comput. Biol. Benjamin Martin, Pablo D. Dans, Milosz Wieczór, Núria Villegas, Isabelle Brun-Heath, Federica Battistini, Montserrat Terrazas, Modesto Orozco
2021	J	`jnl`	The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function. PLoS Comput. Biol. Federica Battistini, Pablo D. Dans, Montserrat Terrazas, Chiara L. Castellazzi, Guillem Portella, Mireia Labrador, Núria Villegas, Isabelle Brun-Heath, Carlos González, Modesto Orozco
2020	J	`jnl`	Molywood: streamlining the design and rendering of molecular movies. Bioinform. Milosz Wieczór, Adam Hospital, Genís Bayarri, Jacek Czub, Modesto Orozco
2019	J	`jnl`	VeriNA3d: an R package for nucleic acids data mining. Bioinform. Diego Gallego, Leonardo Darré, Pablo D. Dans, Modesto Orozco
2017	J	`jnl`	Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs. J. Chem. Inf. Model. Martin Kotev, Pilar Manuel-Manresa, M. Elena Hernando, Vanessa Soto-Cerrato, Modesto Orozco, Roberto Quesada, Ricardo Pérez-Tomás, Victor Guallar
2017	J	`jnl`	PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. Nucleic Acids Res. Víctor López-Ferrando, Andrea M. Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Lluís Gelpí
2016	J	`jnl`	BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. Nucleic Acids Res. Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codó, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Josep Ramón Goñi, Modesto Orozco, Josep Lluís Gelpí
2016	J	`jnl`	Computational Prediction of HIV-1 Resistance to Protease Inhibitors. J. Chem. Inf. Model. Ali Hosseini, Andreu Alibés, Marc Noguera-Julian, Víctor A. Gil, Roger Paredes, Robert Soliva, Modesto Orozco, Victor Guallar
2016	J	`jnl`	The Differential Response of Proteins to Macromolecular Crowding. PLoS Comput. Biol. Michela Candotti, Modesto Orozco
2016	J	`jnl`	pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data. SoftwareX Ardita Shkurti, Josep Ramón Goñi, Pau Andrio, Elena Breitmoser, Iain Bethune, Modesto Orozco, Charles A. Laughton
2015	J	`jnl`	SEABED: Small molEcule activity scanner weB servicE baseD. Bioinform. Carlos Fenollosa, Marcel Otón, Pau Andrio, Jorge Cortés, Modesto Orozco, Josep Ramón Goñi
2013	J	`jnl`	Exploration of conformational transition pathways from coarse-grained simulations. Bioinform. Pedro Sfriso, Adam Hospital, Agustí Emperador, Modesto Orozco
2013	J	`jnl`	Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale. PLoS Comput. Biol. Michela Candotti, Alberto Pérez, Carles Ferrer-Costa, Manuel Rueda, Tim Meyer, Josep Lluís Gelpí, Modesto Orozco
2013	J	`jnl`	NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res. Adam Hospital, Ignacio Faustino, Rosana Collepardo-Guevara, Carlos González, Josep Lluís Gelpí, Modesto Orozco
2013	J	`jnl`	Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations. PLoS Comput. Biol. Guillem Portella, Federica Battistini, Modesto Orozco
2012	J	`jnl`	Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case. PLoS Comput. Biol. Rebeca García-Fandiño, Pau Bernadó, Sara Ayuso-Tejedor, Javier Sancho, Modesto Orozco
2012	J	`jnl`	MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinform. Adam Hospital, Pau Andrio, Carlos Fenollosa, Damjan Cicin-Sain, Modesto Orozco, Josep Lluís Gelpí
2011	J	`jnl`	Nucleotide Binding Switches the Information Flow in Ras GTPases. PLoS Comput. Biol. Francesco Raimondi, Guillem Portella, Modesto Orozco, Francesca Fanelli
2011	J	`jnl`	Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking. J. Chem. Inf. Model. Carles Pons, David Talavera, Xavier de la Cruz, Modesto Orozco, Juan Fernández-Recio
2011	J	`jnl`	nucleR: a package for non-parametric nucleosome positioning. Bioinform. Oscar Flores, Modesto Orozco
2010	J	`jnl`	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. Ignacio Soteras, Modesto Orozco, F. Javier Luque
2009	J	`jnl`	FlexServ: an integrated tool for the analysis of protein flexibility. Bioinform. Jordi Camps, Oliver Carrillo, Agustí Emperador, Laura Orellana, Adam Hospital, Manuel Rueda, Damjan Cicin-Sain, Marco D'Abramo, Josep Lluís Gelpí, Modesto Orozco
2008	J	`jnl`	DNAlive: a tool for the physical analysis of DNA at the genomic scale. Bioinform. Josep Ramón Goñi, Carlos Fenollosa, Alberto Pérez, David Torrents, Modesto Orozco
2007	J	`jnl`	A consensus view of protein dynamics. Proc. Natl. Acad. Sci. USA Manuel Rueda, Carles Ferrer-Costa, Tim Meyer, Alberto Pérez, Jordi Camps, Adam Hospital, Josep Lluís Gelpí, Modesto Orozco
2007	J	`jnl`	A procedure for identifying homologous alternative splicing events. BMC Bioinform. David Talavera, Adam Hospital, Modesto Orozco, Xavier de la Cruz
2007	J	`jnl`	Extension of the MST continuum solvation model to the RM1 semiempirical hamiltonian. J. Comput. Chem. Flavio Forti, Xavier Barril, F. Javier Luque, Modesto Orozco
2007	J	`jnl`	The (In)dependence of Alternative Splicing and Gene Duplication. PLoS Comput. Biol. David Talavera, Christine Vogel, Modesto Orozco, Sarah A. Teichmann, Xavier de la Cruz
2006	J	`jnl`	Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model. J. Comput. Chem. Carles Curutchet, Modesto Orozco, F. Javier Luque, Benedetta Mennucci, Jacopo Tomasi
2005	J	`jnl`	Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient. J. Comput. Aided Mol. Des. Jordi Muñoz-Muriedas, Samantha Perspicace, Nuria Bech, Salvatore Guccione, Modesto Orozco, F. Javier Luque
2005	J	`jnl`	PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinform. Carles Ferrer-Costa, Josep Lluís Gelpí, Leire Zamakola, Ivan Parraga, Xavier de la Cruz, Modesto Orozco
2005	J	`jnl`	PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res. Lucía Conde, Juan M. Vaquerizas, Carles Ferrer-Costa, Xavier de la Cruz, Modesto Orozco, Joaquín Dopazo
2004	—	`conf`	Annotation of Non-Human Pathological Mutations utilising Human-Parameterised Neural Networks. Spanish Bioinformatics Conference Carles Ferrer-Costa, Modesto Orozco, Xavier de la Cruz
2004	—	`conf`	Comparative Study of MAPK 9 Alternative Splicing from Human and Mouse. Spanish Bioinformatics Conference David Talavera, Carles Ferrer-Costa, Modesto Orozco, Xavier de la Cruz
2004	—	`conf`	Comparison of Active Centers of Proteins: The Kinesin Family as a Test Case. Spanish Bioinformatics Conference Antoni Valencia, Martín Pérez, Adam Hospital, Joan Carles Fernández, Elena Manresa, Robert Soliva, Josep Lluís Gelpí, Modesto Orozco
2004	—	`conf`	Hydration Free Energy in Macromolecules. Spanish Bioinformatics Conference Antonio Morreale, Xavier de la Cruz, Tim Meyer, Josep Lluís Gelpí, F. Javier Luque, Modesto Orozco
2004	—	`conf`	Triplex-Forming Sequences in Regulatory Regions. Spanish Bioinformatics Conference Josep Ramón Goñi, Modesto Orozco
2003	J	`jnl`	Continuum and discrete calculation of fractional contributions to solvation free energy. J. Comput. Chem. Antonio Morreale, Josep Lluís Gelpí, F. Javier Luque, Modesto Orozco
2003	J	`jnl`	Electrostatic component of solvation: Comparison of SCRF continuum models. J. Comput. Chem. Carles Curutchet, Christopher J. Cramer, Donald G. Truhlar, Manuel F. Ruiz-López, Daniel Rinaldi, Modesto Orozco, F. Javier Luque
2003	J	`jnl`	Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations. J. Comput. Chem. Carles Curutchet, Josep Maria Bofill, Begoña Hernández, Modesto Orozco, F. Javier Luque
2003	J	`jnl`	Transferability of fragmental contributions to the octanol/water partition coefficient: An NDDO-based MST study. J. Comput. Chem. Carles Curutchet, Albert Salichs, Xavier Barril, Modesto Orozco, Francisco Javier Luque
2002	J	`jnl`	Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study. J. Comput. Aided Mol. Des. Albert Salichs, M. López, V. Segarra, Modesto Orozco, F. Javier Luque
2002	J	`jnl`	Hydrophobic similarity between molecules: A MST-based hydrophobic similarity index. J. Comput. Chem. Jordi Muñoz, Xavier Barril, Begoña Hernández, Modesto Orozco, F. Javier Luque
2002	J	`jnl`	Ligand-induced changes in the binding sites of proteins. Bioinform. Xavier Fradera, Xavier de la Cruz, Carlos H. Tomich P. Silva, Josep Lluís Gelpí, F. Javier Luque, Modesto Orozco
2001	J	`jnl`	Solvation in octanol: parametrization of the continuum MST model. J. Comput. Chem. Carles Curutchet, Modesto Orozco, F. Javier Luque
2000	J	`jnl`	Mixed QM/MM molecular electrostatic potentials. J. Comput. Aided Mol. Des. Begoña Hernández, F. Javier Luque, Modesto Orozco
1999	J	`jnl`	Fractional description of free energies of solvation. J. Comput. Aided Mol. Des. F. Javier Luque, Xavier Barril, Modesto Orozco
1999	J	`jnl`	Monte Carlo-MST: New strategy for representation of solvent configurational space in solution. J. Comput. Chem. Carles Colominas, F. Javier Luque, Modesto Orozco
1999	J	`jnl`	Parametrization of the GMIPp for the study of stacking interactions. J. Comput. Chem. Begoña Hernández, F. Javier Luque, Modesto Orozco
1998	J	`jnl`	Polarization effects in generalized molecular interaction potential: New Hamiltonian for reactivity studies and mixed QM/MM calculations. J. Comput. Chem. F. Javier Luque, Modesto Orozco
1997	J	`jnl`	Role of the tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase. J. Comput. Aided Mol. Des. Begoña Hernández, Modesto Orozco, F. Javier Luque
1997	J	`jnl`	Suitability of density functional methods for calculation of electrostatic properties. J. Comput. Chem. Robert Soliva, Modesto Orozco, F. Javier Luque
1996	J	`jnl`	Extension of MST/SCRF method to organic solvents: Ab initio and semiempirical parametrization for neutral solutes in CCl4. J. Comput. Chem. F. Javier Luque, Margarida Bachs, Carlos Alemán, Modesto Orozco
1996	J	`jnl`	Tautomerism of xanthine and alloxanthine: A model for substrate recognition by xanthine oxidase. J. Comput. Aided Mol. Des. Begoña Hernández, Modesto Orozco, F. Javier Luque
1995	J	`jnl`	Development of Optimized MST/SCRF Methods for Semiempirical Calculations: The MNDO and PM3 Hamilitonians. J. Comput. Chem. Modesto Orozco, Margarida Bachs, F. Javier Luque
1994	J	`jnl`	An Optimized AM1/MST Method for the MST-SCRF Representation of Solvated Systems. J. Comput. Chem. F. Javier Luque, Margarida Bachs, Modesto Orozco
1994	J	`jnl`	Comparison of NDDO and Quasi-Ab Initio Approaches to Compute Semiempirical Molecular Electrostatic Potentials. J. Comput. Chem. Cristóbal Alhambra, Francisco Javier Luque, Modesto Orozco
1994	J	`jnl`	Optimization of Solute Cavities and van der Waals Parameters in Ab Initio MST-SCRF Calculations of Neutral Molecules. J. Comput. Chem. Margarida Bachs, F. Javier Luque, Modesto Orozco
1993	J	`jnl`	A new scaling procedure to correct semiempirical MEP and MEP-derived properties. J. Comput. Aided Mol. Des. Carlos Alemán, F. Javier Luque, Modesto Orozco
1993	J	`jnl`	Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges. J. Comput. Chem. Heather A. Carlson, Toan B. Nguyen, Modesto Orozco, William L. Jorgensen
1993	J	`jnl`	Comparison of 6-31G*-based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules. J. Comput. Chem. Modesto Orozco, William L. Jorgensen, F. Javier Luque
1993	J	`jnl`	Molecular interaction potential: A new tool for the theoretical study of molecular reactivity. J. Comput. Chem. Modesto Orozco, F. Javier Luque
1993	J	`jnl`	Suitability of the PM3-derived molecular electrostatic potentials. J. Comput. Chem. Carlos Alemán, F. Javier Luque, Modesto Orozco
1992	J	`jnl`	On the suitability of semiempirical calculations as sources of force field parameters. J. Comput. Aided Mol. Des. Carlos Alemán, Modesto Orozco
1990	J	`jnl`	A practical procedure for the determination of electrostatic charges of large molecules. J. Comput. Aided Mol. Des. Modesto Orozco, F. Javier Luque
1989	J	`jnl`	POEAMS: program for outliers elimination in 'anomalous' multidimensional space. Comput. Appl. Biosci. Modesto Orozco, F. Javier Luque
1989	J	`jnl`	TEFOOL/2: a program for theoretical drug design on microcomputers. Comput. Appl. Biosci. Modesto Orozco, Rafael Franco
1988	J	`jnl`	POEMS: program for outliers elimination in multidimensional space. Comput. Appl. Biosci. Modesto Orozco, F. Javier Luque