Modesto Orozco

发表

A practical procedure for the determination of electrostatic charges of large molecules

F. Javier Luque, F. J. Luque, Modesto Orozco, 1990, J. Comput. Aided Mol. Des..

PMut2: a web-based tool for predicting pathological mutations on proteins

Modesto Orozco, Víctor López-Ferrando, Xavier de la Cruz, 2015 .

Target flexibility: an emerging consideration in drug discovery and design.

Holger Gohlke, Garrett M Morris, Francesca Fanelli, 2008, Journal of medicinal chemistry.

F. Javier Luque, Xavier Barril, Modesto Orozco, 2002, J. Comput. Chem..

FlexServ: an integrated tool for the analysis of protein flexibility

Modesto Orozco, Jordi Camps, Oliver Carrillo, 2009, Bioinform..

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

Jordi Torres, Yolanda Becerra, Modesto Orozco, 2015, Nucleic Acids Res..

Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale

Modesto Orozco, Manuel Rueda, Josep Lluis Gelpí, 2013, PLoS Comput. Biol..

A Multilevel Strategy for the Exploration of the Conformational Flexibility of Small Molecules.

Claudio N. Cavasotto, Claudio N Cavasotto, Xavier Barril, 2012, Journal of chemical theory and computation.

On the suitability of semiempirical calculations as sources of force field parameters

Modesto Orozco, Carlos Alemán, 1992, J. Comput. Aided Mol. Des..

Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking

Carles Pons, Modesto Orozco, Xavier de la Cruz, 2011, J. Chem. Inf. Model..

Role of the tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase

Modesto Orozco, Begoña Hernández, Francisco J. Luque, 1997, J. Comput. Aided Mol. Des..

Web-based tool for the annotation of pathological variants on proteins: PMut 2017 update

Modesto Orozco, Víctor López-Ferrando, Xavier de la Cruz, 2017 .

Triplex-Forming Sequences in Regulatory Regions

Modesto Orozco, Josep Ramón Goñi, 2004, Spanish Bioinformatics Conference.

Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.

Modesto Orozco, Athi N. Naganathan, Oliver Carrillo, 2011, Advances in protein chemistry and structural biology.

Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study

F. Javier Luque, F. J. Luque, Modesto Orozco, 2002, J. Comput. Aided Mol. Des..

Approaching Elastic Network Models to Molecular Dynamics Flexibility.

Modesto Orozco, Pablo Chacón, Laura Orellana, 2010, Journal of chemical theory and computation.

Molywood: streamlining the design and rendering of molecular movies

Modesto Orozco, Jacek Czub, Adam Hospital, 2020, Bioinform..

MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.

Modesto Orozco, Dmitry Repchevsky, Jordi Camps, 2010, Structure.

Efficient Relaxation of Protein-Protein Interfaces by Discrete Molecular Dynamics Simulations.

Albert Solernou, Modesto Orozco, Juan Fernandez-Recio, 2013, Journal of chemical theory and computation.

Electrostatic component of solvation: Comparison of SCRF continuum models

Manuel F. Ruiz-López, F. Javier Luque, F. J. Luque, 2003, J. Comput. Chem..

Comparison of Active Centers of Proteins: The Kinesin Family as a Test Case

Modesto Orozco, Adam Hospital, Josep Lluis Gelpí, 2004, Spanish Bioinformatics Conference.

Tautomerism of xanthine and alloxanthine: A model for substrate recognition by xanthine oxidase

F. Javier Luque, Modesto Orozco, Begoña Hernández, 1996, J. Comput. Aided Mol. Des..

Ab initio study of bond stretching: Implications in force‐field parametrization for molecular mechanics and dynamics

F. J. Luque, Modesto Orozco, F.J. Luque, 1993, J. Comput. Chem..

Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient

F. Javier Luque, F. J. Luque, Salvatore Guccione, 2005, J. Comput. Aided Mol. Des..

Fractional description of free energies of solvation

F. Javier Luque, Xavier Barril, Modesto Orozco, 1999, J. Comput. Aided Mol. Des..

BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows

Carole Goble, Stian Soiland-Reyes, Rosa M. Badia, 2019, Scientific Data.

Comparative Study of MAPK 9 Alternative Splicing from Human and Mouse

Modesto Orozco, Xavier de la Cruz, Carles Ferrer-Costa, 2004, Spanish Bioinformatics Conference.

Mixed QM/MM molecular electrostatic potentials

F. Javier Luque, F. J. Luque, Modesto Orozco, 2000, J. Comput. Aided Mol. Des..

POEMS: program for outliers elimination in multidimensional space

F. Javier Luque, Modesto Orozco, 1988, Comput. Appl. Biosci..

Optimization of solute cavities and van der Waals parameters in ab initio MST‐SCRF calculations of neutral molecules

F. Javier Luque, F. J. Luque, Modesto Orozco, 1994, J. Comput. Chem..

VeriNA3d: an R package for nucleic acids data mining

Modesto Orozco, Leonardo Darré, Diego Gallego, 2019, Bioinform..

Transferability of fragmental contributions to the octanol/water partition coefficient: An NDDO‐based MST study

F. Javier Luque, Xavier Barril, F. J. Luque, 2003, J. Comput. Chem..

Molecular interaction potential: A new tool for the theoretical study of molecular reactivity

F. Javier Luque, F. J. Luque, Modesto Orozco, 1993, J. Comput. Chem..

TEFOOL/2: a program for theoretical drug design on microcomputers

Modesto Orozco, Rafael Franco, 1989, Comput. Appl. Biosci..

A consensus view of protein dynamics

Modesto Orozco, Jordi Camps, Adam Hospital, 2007, Proceedings of the National Academy of Sciences.

Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies

F. Javier Luque, F. J. Luque, Modesto Orozco, 2010, J. Comput. Aided Mol. Des..

Theoretical and physical chemistry

Peter Willett, Walter Thiel, Modesto Orozco, 2014 .

Data Mining of Molecular Dynamics Trajectories of Nucleic Acids

F. J. Luque, Modesto Orozco, Carles Ferrer, 2006, Journal of biomolecular structure & dynamics.

Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model

Jacopo Tomasi, F. Javier Luque, F. J. Luque, 2006, J. Comput. Chem..

NAFlex: a web server for the study of nucleic acid flexibility

Carlos González, Modesto Orozco, Adam Hospital, 2013, Nucleic Acids Res..

Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.

Modesto Orozco, Agustí Emperador, M. Orozco, 2017, Journal of chemical theory and computation.

An optimized AM1/MST method for the MST‐SCRF representation of solvated systems

F. J. Luque, Modesto Orozco, F. J. Luque, 1994, J. Comput. Chem..

Essential Dynamics: A Tool for Efficient Trajectory Compression and Management.

Charles A Laughton, Modesto Orozco, F Javier Luque, 2006, Journal of chemical theory and computation.

Polarization effects in generalized molecular interaction potential: New Hamiltonian for reactivity studies and mixed QM/MM calculations

F. Javier Luque, Modesto Orozco, 1998, J. Comput. Chem..

Solvation in octanol: parametrization of the continuum MST model

F. Javier Luque, F. J. Luque, Modesto Orozco, 2001, J. Comput. Chem..

A procedure for identifying homologous alternative splicing events

Modesto Orozco, Xavier de la Cruz, Adam Hospital, 2007, BMC Bioinformatics.

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update

Andrea Gazzo, Modesto Orozco, Víctor López-Ferrando, 2017, Nucleic Acids Res..

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

Alfonso Valencia, Philippe Bardou, Arcadi Navarro, 2008, Briefings in bioinformatics.

Development of optimized MST/SCRF methods for semiempirical calculations: The MNDO and PM3 Hamiltonians

F. Javier Luque, F. J. Luque, Modesto Orozco, 1995, J. Comput. Chem..

Ligand-induced changes in the binding sites of proteins

F. Javier Luque, F. J. Luque, Modesto Orozco, 2002, Bioinform..

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Arne Elofsson, Matthias Rarey, Anastassis Perrakis, 2020, F1000Research.

BIOACTIVE CONFORMATIONAL ENSEMBLE SERVER AND DATABASE. A PUBLIC FRAMEWORK TO SPEED UP IN SILICO DRUG DISCOVERY.

Robert Soliva, Modesto Orozco, David Moreno, 2020, Journal of chemical theory and computation.

Monte Carlo-MST: New strategy for representation of solvent configurational space in solution

F. Javier Luque, Modesto Orozco, Carles Colominas, 1999, J. Comput. Chem..

Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case

Modesto Orozco, Pau Bernadó, Rebeca García-Fandiño, 2012, PLoS Comput. Biol..

A new scaling procedure to correct semiempirical MEP and MEP-derived properties

F. Javier Luque, F. J. Luque, Modesto Orozco, 1993, J. Comput. Aided Mol. Des..

Polarization effects in molecular interactions

F. Javier Luque, Christophe Chipot, F. J. Luque, 2011 .

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

Modesto Orozco, Oliver Carrillo, Erik Lindahl, 2016, Nature Communications.

PMUT: a web-based tool for the annotation of pathological mutations on proteins

Modesto Orozco, Xavier de la Cruz, Josep Lluis Gelpí, 2005, Bioinform..

SEABED: Small molEcule activity scanner weB servicE baseD

Jorge Cortés, Modesto Orozco, Pau Andrio, 2014, Bioinform..

Continuum and discrete calculation of fractional contributions to solvation free energy

F. Javier Luque, F. J. Luque, Modesto Orozco, 2003, J. Comput. Chem..

Suitability of density functional methods for calculation of electrostatic properties

F. Javier Luque, Modesto Orozco, Robert Soliva, 1997, J. Comput. Chem..

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations

Modesto Orozco, Adam Hospital, Damjan Cicin-Sain, 2012, Bioinform..

The (In)dependence of Alternative Splicing and Gene Duplication

Sarah A. Teichmann, Modesto Orozco, Xavier de la Cruz, 2007, PLoS Comput. Biol..

Hydration Free Energy in Macromolecules

F. Javier Luque, Modesto Orozco, Xavier de la Cruz, 2004, Spanish Bioinformatics Conference.

Comparison of 6‐31G*‐based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules

F. Javier Luque, William L. Jorgensen, F. J. Luque, 1993, J. Comput. Chem..

Annotation of Non-Human Pathological Mutations utilising Human-Parameterised Neural Networks

Modesto Orozco, Xavier de la Cruz, Carles Ferrer-Costa, 2004, Spanish Bioinformatics Conference.

Extension of MST/SCRF method to organic solvents: Ab initio and semiempirical parametrization for neutral solutes in CCl4

F. Javier Luque, Modesto Orozco, Carlos Alemán, 1996, J. Comput. Chem..

nucleR: a package for non-parametric nucleosome positioning

Oscar Flores, Modesto Orozco, M. Orozco, 2011, Bioinform..

POEAMS: program for outliers elimination in 'anomalous' multidimensional space

F. Javier Luque, Modesto Orozco, 1989, Comput. Appl. Biosci..

Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings.

Charles A Laughton, Modesto Orozco, Oliver Carrillo, 2012, Journal of chemical theory and computation.

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes

Joaquín Dopazo, Modesto Orozco, Xavier de la Cruz, 2005, Nucleic Acids Res..

Comparison of NDDO and quasi‐ab initio approaches to compute semiempirical molecular electrostatic potentials

F. Javier Luque, Modesto Orozco, Cristóbal Alhambra, 1994, J. Comput. Chem..

Accuracy of free energies of hydration for organic molecules from 6‐31g*‐derived partial charges

Heather A. Carlson, William L. Jorgensen, Modesto Orozco, 1993, J. Comput. Chem..

Nucleotide Binding Switches the Information Flow in Ras GTPases

Francesca Fanelli, Modesto Orozco, Francesco Raimondi, 2011, PLoS Comput. Biol..

Computational Prediction of HIV-1 Resistance to Protease Inhibitors

Victor Guallar, Robert Soliva, Modesto Orozco, 2016, J. Chem. Inf. Model..

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

Modesto Orozco, Andrzej Kolinski, Sebastian Kmiecik, 2013, Journal of chemical theory and computation.

Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations

Modesto Orozco, Federica Battistini, Guillem Portella, 2013, PLoS Comput. Biol..

DNAlive: a tool for the physical analysis of DNA at the genomic scale

Modesto Orozco, Josep Ramón Goñi, Alberto Pérez, 2008, Bioinform..

Exploration of conformational transition pathways from coarse-grained simulations

Modesto Orozco, Agustí Emperador, Adam Hospital, 2013, Bioinform..

The Differential Response of Proteins to Macromolecular Crowding

Modesto Orozco, Michela Candotti, 2016, PLoS Comput. Biol..

Parametrization of the GMIPp for the study of stacking interactions

F. Javier Luque, F. J. Luque, Modesto Orozco, 1999, J. Comput. Chem..

Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations

F. Javier Luque, F. J. Luque, Modesto Orozco, 2003, J. Comput. Chem..

Extension of the MST continuum solvation model to the RM1 semiempirical hamiltonian

F. Javier Luque, Xavier Barril, F. J. Luque, 2008, J. Comput. Chem..

Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer's disease.

F. J. Luque, Modesto Orozco, F Javier Luque, 2005, Journal of medicinal chemistry.

Long-timescale dynamics of the Drew–Dickerson dodecamer

Modesto Orozco, Adam Hospital, Pablo D. Dans, 2016, Nucleic acids research.

Response to "Comment on `New strategies to incorporate the solvent polarization in self-consistent reaction field and free-energy perturbation simulations' " [J. Chem. Phys. 107, 1291 (1997)]

Modesto Orozco, Josep Maria Bofill, Francisco Javier Luque, 1997 .

THEORETICAL STUDY OF THE TAUTOMERISM AND PROTONATION OF 7-AMINOPYRAZOLOPYRIMIDINE IN THE GAS PHASE AND IN AQUEOUS SOLUTION

F. J. Luque, Modesto Orozco, Francisco Javier Luque, 1995 .

Effect of solvation on the shapes, sizes, and anisotropies of polyatomic anions via molecular electrostatic potential topography: An ab initio self‐consistent reaction field approach

Shridhar R. Gadre, F. J. Luque, Modesto Orozco, 1994 .

Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies.

F. J. Luque, Modesto Orozco, Flavio Forti, 2009, The journal of physical chemistry. B.

Suitability of density functional methods for calculation of electrostatic properties

F. Javier Luque, Robert Soliva, F. J. Luque, 1997, J. Comput. Chem..

Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water

Modesto Orozco, Charles A. Laughton, Agnes Noy, 2007, Nucleic acids research.

Challenges of docking in large, flexible and promiscuous binding sites.

Martin Kotev, Robert Soliva, Modesto Orozco, 2016, Bioorganic & medicinal chemistry.

GRID‐MD—A tool for massive simulation of protein channels

Modesto Orozco, Oliver Carrillo, M. Orozco, 2008, Proteins.

Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species.

Modesto Orozco, Xavier de la Cruz, David Talavera, 2004, Journal of molecular biology.

Extension of the MST model to the IEF formalism: HF and B3LYP parametrizations

F. Javier Luque, F. J. Luque, Modesto Orozco, 2005 .

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Daniel Svozil, Charles A Laughton, Modesto Orozco, 2007, Biophysical journal.

Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily.

Francesca Fanelli, Modesto Orozco, Francesco Raimondi, 2010, Structure.

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

Daniel Jost, Modesto Orozco, Marc A Marti-Renom, 2020, Molecular cell.

SDS-PAGE analysis of Aβ oligomers is disserving research into Alzheimer´s disease: appealing for ESI-IM-MS

Modesto Orozco, Marta Vilaseca, M. Orozco, 2015, Scientific Reports.

A practical approach to the computation of the electrostatic energy in large molecules

F. J. Luque, Modesto Orozco, Francisco Javier Luque, 1992 .

Molecular Solvation Potential. A New Tool for the Quantum Mechanical Description of Hydration in Organic and Bioorganic Molecules

Modesto Orozco, Francisco Javier Luque, C. Alhambra, 1995 .

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

Modesto Orozco, Federica Battistini, Montserrat Soler-López, 2011, BMC Genomics.

Chapter 7:Molecular Modelling of Nucleic Acids

Modesto Orozco, Pablo D. Dans, Leonardo Darré, 2017 .

Ligand‐induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin‐N

F. J. Luque, Modesto Orozco, F Javier Luque, 2006, Proteins.

Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations.

Christophe Chipot, Modesto Orozco, Carles Curutchet, 2007, Journal of chemical theory and computation.

Nucleosome architecture throughout the cell cycle

Modesto Orozco, Montserrat Soler-López, M. Orozco, 2016, Scientific Reports.

Induction effects in metal cation-benzene complexes.

F. J. Luque, Modesto Orozco, F Javier Luque, 2008, Physical chemistry chemical physics : PCCP.

How accurate are accurate force-fields for B-DNA?

Modesto Orozco, Adam Hospital, Pablo D. Dans, 2017, Nucleic acids research.

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.

Daniel Svozil, F. J. Luque, Modesto Orozco, 2008, The journal of physical chemistry. B.

Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA

Modesto Orozco, Federica Battistini, Richard Lavery, 2014, Nucleic acids research.

An atomistic view to the gas phase proteome.

Modesto Orozco, Xavier de la Cruz, Tim Meyer, 2009, Structure.

Ab Initio Study of Stacking Interactions in A- and B-DNA

Modesto Orozco, Francisco Javier Luque, M. Orozco, 1997 .

Molecular dynamics study of 2rotaxanes: influence of solvation and cation on co-conformation.

F. J. Luque, Modesto Orozco, Xavier Fradera, 2003, The Journal of organic chemistry.

Recent advances in the study of nucleic acid flexibility by molecular dynamics.

Modesto Orozco, Agnes Noy, M. Orozco, 2008, Current opinion in structural biology.

Multicentric charges for the accurate representation of electrostatic interactions in force-field calculations for small molecules

Modesto Orozco, Carlos Alemán, Francisco Javier Luque, 1994 .

Towards a molecular dynamics consensus view of B-DNA flexibility

F. Javier Luque, F. J. Luque, Modesto Orozco, 2008, Nucleic acids research.

Theoretical study of N-methylacetamide in vacuum and aqueous solution : implications for the peptide bond isomerization

Modesto Orozco, Francisco Javier Luque, 1993 .

Alternative Splicing of Transcription Factors' Genes: Beyond the Increase of Proteome Diversity

Modesto Orozco, Xavier de la Cruz, David Talavera, 2009, Comparative and functional genomics.

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

Modesto Orozco, Agustí Emperador, Josep Lluis Gelpí, 2015, Journal of chemical theory and computation.

SCRF calculation of the effect of water on the topology of the molecular electrostatic potential

Shridhar R. Gadre, F. J. Luque, Modesto Orozco, 1993 .

Determining promoter location based on DNA structure first-principles calculations

Modesto Orozco, David Torrents, D. Torrents, 2007, Genome Biology.

Polarization effects in generalized molecular interaction potential: New Hamiltonian for reactivity studies and mixed QM/MM calculations

F. Javier Luque, Modesto Orozco, 1998 .

Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.

F. J. Luque, Modesto Orozco, Nicola G A Abrescia, 2003, Journal of the American Chemical Society.

Solvent Effects in Chloroform Solution: Parametrization of the MST/SCRF Continuum Model

Modesto Orozco, Carlos Alemán, Y. Zhang, 1996 .

Observation of Spontaneous Base Pair Breathing Events in the Molecular Dynamics Simulation of a Difluorotoluene-Containing DNA Oligonucleotide

F. Javier Luque, Modesto Orozco, Edward C. Sherer, 1999 .

Frontiers in molecular dynamics simulations of DNA.

F. J. Luque, Modesto Orozco, F Javier Luque, 2012, Accounts of chemical research.

Nature of minor-groove binders-DNA complexes in the gas phase.

F. J. Luque, Modesto Orozco, F Javier Luque, 2005, Journal of the American Chemical Society.

Tautomerism of Xanthine Oxidase Substrates Hypoxanthine and Allopurinol

F. J. Luque, Modesto Orozco, Begoña Hernández, 1996 .

Optimization of the cavity size for ab initio MST-SCRF calculations of monovalent ions

F. J. Luque, Modesto Orozco, Francisco J. Luque, 1994 .

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.

Michal Otyepka, Modesto Orozco, Thomas E. Cheatham, 2010, Journal of chemical theory and computation.

Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution.

Modesto Orozco, Marco D'Abramo, M. Orozco, 2009, Journal of the American Chemical Society.

Partition of protein solvation into group contributions from molecular dynamics simulations

F. J. Luque, Modesto Orozco, Antonio Morreale, 2004, Proteins.

Theoretical Methods for the Simulation of Nucleic Acids

F. Javier Luque, Modesto Orozco, Agnes Noy, 2004 .

CAVITATION CONTRIBUTION TO THE FREE ENERGY OF SOLVATION. COMPARISON OF DIFFERENT FORMALISMS IN THE CONTEXT OF MST CALCULATIONS

F. Javier Luque, F. J. Luque, Modesto Orozco, 1999 .

Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family.

Carmen Almansa, Robert Soliva, Modesto Orozco, 2007, Journal of medicinal chemistry.

Comparative study of the molecular electrostatic potential obtained from different wavefunctions. Reliability of the semiempirical MNDO wavefunction

F. J. Luque, Modesto Orozco, Francesc Illas, 1990 .

Effect of electron correlation on the electrostatic potential distribution of molecules

Modesto Orozco, Francesc Illas, Francisco Javier Luque, 1991 .

A Topological Analysis of Electron Density in Cation−π Complexes

F. J. Luque, Modesto Orozco, Francisco J. Luque, 1999 .

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads

Modesto Orozco, David Torrents, Montserrat Puiggròs, 2014, Nature Biotechnology.

Protein flexibility from discrete molecular dynamics simulations using quasi‐physical potentials

Modesto Orozco, Agustí Emperador, Tim Meyer, 2010, Proteins.

Structure, recognition properties, and flexibility of the DNA.RNA hybrid.

F. J. Luque, Modesto Orozco, F Javier Luque, 2005, Journal of the American Chemical Society.

An AM1-SCRF approach to the study of changes in molecular properties induced by solvent

F. J. Luque, Modesto Orozco, Francisco Javier Luque, 1993 .

United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials.

Modesto Orozco, Agustí Emperador, Tim Meyer, 2008, Journal of chemical theory and computation.

TAUTOMERISM AND PROTONATION OF GUANINE AND CYTOSINE. IMPLICATIONS IN THE FORMATION OF HYDROGEN-BONDED COMPLEXES

F. J. Luque, Modesto Orozco, Carles Colominas, 1996 .

Beyond the Continuum Approach

Modesto Orozco, Ignacio Fdez. Galván, Thom Vreven, 2007 .

Reliability of MEP and MEP-derived properties computed from DFT methods for molecules containing P, S and CL

Robert Soliva, Modesto Orozco, Francisco Javier Luque, 1997 .

Towards a consensus view of RNA flexibility

Modesto Orozco, Ignacio Faustino, Alberto Perez, 2010 .

Multiscale simulation of DNA.

Modesto Orozco, Pablo D Dans, Hansel Gómez, 2016, Current opinion in structural biology.

Perturbation approach to combined QM/MM simulation of solute-solvent interactions in solution

F. Javier Luque, Modesto Orozco, Jiali Gao, 2003 .

Theoretical studies on the inhibition mechanism of cyclooxygenase-2. Is there a unique recognition site?

Carmen Almansa, Robert Soliva, F. J. Luque, 2003, Journal of medicinal chemistry.

Role of Intramolecular Hydrogen Bonds in the Intermolecular Hydrogen Bonding of Carbohydrates

Modesto Orozco, Manuela López de la Paz, F. Javier Luque, 1998 .

Reliability of the AM1 wavefunction to compute molecular electrostatic potentials

F. J. Luque, Modesto Orozco, Francisco Javier Luque, 1990 .

Molecular Dynamics Studies of DNA A-Tract Structure and Flexibility

Robert Soliva, Modesto Orozco, Sarah A. Harris, 1999 .

Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

Charles A Laughton, Modesto Orozco, Manuel Rueda, 2004, Biophysical journal.

On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges

Modesto Orozco, Francisco Javier Luque, 1990 .

A fast method for the determination of fractional contributions to solvation in proteins

Robert Soliva, F. J. Luque, Modesto Orozco, 2006, Protein science : a publication of the Protein Society.

Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering.

Modesto Orozco, Pau Bernadó, Javier Sancho, 2011, Journal of molecular biology.

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

Donald G Truhlar, Modesto Orozco, Jiali Gao, 2009, Journal of chemical theory and computation.

Comparison of molecular dynamics and superfamily spaces of protein domain deformation

Modesto Orozco, Manuel Rueda, Isabel Cuesta, 2009, BMC Structural Biology.

Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling

Juan González-Vallinas, Modesto Orozco, Eulàlia de Nadal, 2012, Genome Biology.

New strategies to incorporate the solvent polarization in self‐consistent reaction field and free‐energy perturbation simulations

Modesto Orozco, Josep Maria Bofill, Francisco Javier Luque, 1995 .

Proteins in the gas phase

Helmut Grubmüller, Modesto Orozco, Tim Meyer, 2013 .

Generalized linear response approximation in discrete methods

F. J. Luque, Modesto Orozco, Francisco Javier Luque, 1997 .

Linear response theory: An alternative to PB and GB methods for the analysis of molecular dynamics trajectories?

F. J. Luque, Modesto Orozco, Antonio Morreale, 2004, Proteins.

A theoretical view of protein dynamics.

Modesto Orozco, M. Orozco, 2014, Chemical Society reviews.

Unravelling the hidden DNA structural/physical code provides novel insights on promoter location

Modesto Orozco, David Torrents, Roderic Guigó, 2013, Nucleic acids research.

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study.

Tamar Schlick, Michele Vendruscolo, Modesto Orozco, 2015, Journal of the American Chemical Society.

Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives.

Modesto Orozco, F Javier Luque, Carlos González, 2002, Journal of the American Chemical Society.

Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design.

Modesto Orozco, Rima Chaudhuri, Oliver Carrillo, 2012, Journal of chemical theory and computation.

THE POLARIZATION CONTRIBUTION TO THE FREE ENERGY OF HYDRATION

Modesto Orozco, Jiali Gao, Francisco Javier Luque, 1995 .

Small Details Matter: The 2'-Hydroxyl as a Conformational Switch in RNA.

Modesto Orozco, Adam Hospital, Leonardo Darré, 2016, Journal of the American Chemical Society.

Self‐consistent reaction field computation of the reactive characteristics of DNA bases in water

F. J. Luque, Modesto Orozco, Francisco Javier Luque, 1993 .

Semiclassical-Continuum Approach to the Electrostatic Free Energy of Solvation

Modesto Orozco, and F. J. Luque, 1997 .

Multiple routes to characterize the folding of a small DNA hairpin.

Modesto Orozco, Guillem Portella, G. Portella, 2010, Angewandte Chemie.

Exploring the Essential Dynamics of B-DNA.

Modesto Orozco, Xavier de la Cruz, Manuel Rueda, 2005, Journal of chemical theory and computation.

Continuum solvation models: Dissecting the free energy of solvation

F. Javier Luque, F. J. Luque, Modesto Orozco, 2003 .

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

David A. Case, Modesto Orozco, Thomas C. Bishop, 2014, Nucleic acids research.

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions

Modesto Orozco, Juan M. Vaquerizas, Joaquin Dopazo, 2006, BMC Genomics.

On the use of mixed basis sets to compute accurate molecular electrostatic potentials

F. J. Luque, Modesto Orozco, Francisco Javier Luque, 1989 .

Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data.

Dmitri I Svergun, Juan Fernández-Recio, Modesto Orozco, 2010, Journal of molecular biology.

Molecular Dynamics Simulations in Aqueous Solution of Triple Helices Containing d(G·C·C) Trios

F. Javier Luque, Robert Soliva, F. J. Luque, 1998 .

Theoretical study of the hydroxyl nucleophilic attack on the 6-aminopyrimidine molecule: functional implications in the reaction mechanism of nucleoside deaminative enzymes

Modesto Orozco, Rafael Franco, Enric I. Canela, 1990 .

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

Modesto Orozco, Leonardo Darré, Massimiliano Porrini, 2017, bioRxiv.

Extension of MST/SCRF method to organic solvents: Ab initio and semiempirical parametrization for neutral solutes in CCl4

F. J. Luque, Modesto Orozco, Carlos Alemán, 1996, J. Comput. Chem..

Ab initio study of naphtho-homologated DNA bases.

Modesto Orozco, Miguel Fuentes-Cabrera, F Javier Luque, 2008, The journal of physical chemistry. B.

Impact of methylation on the physical properties of DNA.

Modesto Orozco, David Torrents, Ramon Eritja, 2012, Biophysical journal.

A Priori Prediction of Substituent and Solvent Effects in the Basicity of Nitriles

Modesto Orozco, José I. Borrell, Jordi Teixidó, 1998 .

Partitioning of Free Energies of Solvation into Fragment Contributions: Applications in Drug Design

Xavier Barril, F. J. Luque, Modesto Orozco, 2001 .

Ensemble Docking from Homology Models.

Xavier Barril, Modesto Orozco, Eva Maria Novoa, 2010, Journal of chemical theory and computation.

Simplified descriptions of the topological distribution of hydrophilic/hydrophobic characteristics of molecules

F. Javier Luque, Xavier Barril, F. J. Luque, 2000 .

Monte Carlo–MST: New strategy for representation of solvent configurational space in solution

Modesto Orozco, Carles Colominas, F. Luque, 1999, Journal of computational chemistry.

Relative flexibility of DNA and RNA: a molecular dynamics study.

Modesto Orozco, Filip Lankas, Agnes Noy, 2004, Journal of molecular biology.

Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.

Modesto Orozco, Agustí Emperador, Manuel Rueda, 2008, Biophysical journal.

The structure and dynamics of DNA in the gas phase.

F. J. Luque, Modesto Orozco, F Javier Luque, 2003, Journal of the American Chemical Society.

Molecular Dynamics Simulations of the Unfolding of Barnase in Water and 8 M

William L. Jorgensen, Modesto Orozco, Julian Tirado-Rives, 1997 .

Inntags: small self-structured epitopes for innocuous protein tagging

Modesto Orozco, Josep Lluís Gelpí, Ricardo Jara, 2015, Nature Methods.

Allosterism and signal transfer in DNA

Modesto Orozco, Pablo D Dans, M. Orozco, 2018, Nucleic acids research.

Saturation of recognition elements blocks evolution of new tRNA identities

Modesto Orozco, Fyodor A. Kondrashov, Pablo D. Dans, 2016, Science Advances.

Induced dipole moment and atomic charges based on average electrostatic potentials in aqueous solution

F. J. Luque, Modesto Orozco, Jiali Gao, 1993 .

Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study.

Pavel Hobza, F. J. Luque, Modesto Orozco, 2005, Chemistry.

Modesto Orozco, Laura Orellana, Xavier Salvatella, 2014, Nature Communications.

Structure and Properties of DNA in Apolar Solvents

Modesto Orozco, David J. Wales, Debayan Chakraborty, 2014, The journal of physical chemistry. B.

Toward a consensus view of duplex RNA flexibility.

Modesto Orozco, Ignacio Faustino, M. Orozco, 2010, Biophysical journal.

Fuzziness and noise in nucleosomal architecture

Modesto Orozco, Montserrat Soler-López, M. Orozco, 2014, Nucleic acids research.

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia

Alfonso Valencia, Modesto Orozco, Brandy Klotzle, 2012, Nature Genetics.

Exploring polymorphisms in B-DNA helical conformations

Modesto Orozco, Pablo D. Dans, Richard Lavery, 2012, Nucleic acids research.

Interactions of Nucleic Acid Bases: The Role of Solvent

F. Javier Luque, Modesto Orozco, Begoña Hernández, 1999 .

Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins.

Modesto Orozco, Patrick Aloy, Roberto Mosca, 2016, Structure.

The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding.

Modesto Orozco, Athi N. Naganathan, Athi N Naganathan, 2011, Journal of the American Chemical Society.

A new strategy for the representation of environment effects in semi-empirical calculations based on Dewar's Hamiltonians

F. J. Luque, Modesto Orozco, Francisco Javier Luque, 1992 .

Prediction of Conformational Free Energy Differences of Solutes in Solution∶ An MC-MST Study

Modesto Orozco, Begoña Hernández, Carles Curutchet, 2002 .

COCO: A simple tool to enrich the representation of conformational variability in NMR structures

Charles A Laughton, Modesto Orozco, Wim Vranken, 2009, Proteins.

A hydrophobic similarity analysis of solvation effects on nucleic acid bases

Xavier Barril, F. J. Luque, Modesto Orozco, 2007, Journal of molecular modeling.