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Modesto Orozco

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Nerea Martín-Pintado; Modesto Orozco; Guillem Portella; Maryam Yahyaee-Anzahaee; Masad J Damha; Glen F Deleavey; Carlos González
Dramatic effect of furanose C2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom.
Michela Candotti; Santiago Esteban-Martín; Xavier Salvatella; Modesto Orozco
Toward an atomistic description of the urea-denatured state of proteins.
Eduard Gracia; Carme Lluís; Josefa Mallol; Peter J McCormick; Modesto Orozco; Antoni Cortés; Francesca Fanelli; Daniel Farré; Carles Ferrer-Costa; Rafael Franco; Enric I Canela; Vicent Casadó
The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors.

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2013: Nerea Martín-Pintado; Modesto Orozco; Guillem Portella; Maryam Yahyaee-Anzahaee; Masad J Damha; Glen F Deleavey; Carlos González
Dramatic effect of furanose C2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom.
Journal of the American Chemical Society 2013;135(14):5344-7.
2013: Michela Candotti; Santiago Esteban-Martín; Xavier Salvatella; Modesto Orozco
Toward an atomistic description of the urea-denatured state of proteins.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(15):5933-8.
2013: Eduard Gracia; Carme Lluís; Josefa Mallol; Peter J McCormick; Modesto Orozco; Antoni Cortés; Francesca Fanelli; Daniel Farré; Carles Ferrer-Costa; Rafael Franco; Enric I Canela; Vicent Casadó
The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2013;27(3):1048-61.
2013: Modesto Orozco
The dynamic view of proteins: Comment on "Comparing proteins to their internal dynamics: Exploring structure-function relationships beyond static structural alignments".
Physics of life reviews 2013;10(1):29-30.
2013: Simone Sciabola; Qing Cao; Ignacio Faustino; Modesto Orozco; Robert V Stanton
Improved nucleic acid descriptors for siRNA efficacy prediction.
Nucleic acids research 2013;41(3):1383-94.
2012: Pablo D Dans; Ignacio Faustino; Richard Lavery; Alberto Pérez; Modesto Orozco
Exploring polymorphisms in B-DNA helical conformations.
Nucleic acids research 2012;40(21):10668-78.
2012: Alberto Pérez; Maria Luz Ruiz; Montserrat Soler-López; David Torrents; Federica Battistini; Chiara Lara Castellazzi; Kathryn Collinet; Ozgen Deniz; Ramon Eritja; Oscar Flores; Modesto Orozco
Impact of methylation on the physical properties of DNA.
Biophysical journal 2012;102(9):2140-8.
2012: Adam Hospital; Modesto Orozco; Pau Andrio; Damjan Cicin-Sain; Carles Fenollosa; Josep Lluis Gelpí
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.
Bioinformatics (Oxford, England) 2012;28(9):1278-9.
2012: Rebeca García-Fandiño; Sara Ayuso-Tejedor; Pau Bernadó; Javier Sancho; Modesto Orozco
Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case.
PLoS computational biology 2012;8(8):e1002647.
2011: José Ramón Blas; Miguel Fuentes-Cabrera; Oscar Huertas; Pablo Ordejón; Modesto Orozco; Bobby G Sumpter; Carolina Tabares; F Javier Luque
Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases.
The journal of physical chemistry. A 2011;115(41):11344-54.
2011: Oscar Flores; Modesto Orozco
nucleR: a package for non-parametric nucleosome positioning.
Bioinformatics (Oxford, England) 2011;27(15):2149-50.
2011: Marco D'Abramo; Modesto Orozco; Andrea Amadei
Effects of local electric fields on the redox free energy of single stranded DNA.
Chemical communications (Cambridge, England) 2011;47(9):2646-8.
2011: Sara Ayuso-Tejedor; Rebeca García-Fandiño; Modesto Orozco; Javier Sancho; Pau Bernadó
Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering.
Journal of molecular biology 2011;406(4):604-19.
2011: Modesto Orozco; Oliver Carrillo; Agustí Emperador; Adam Hospital; Athi N Naganathan; Laura Orellana; Josep Lluis Gelpí
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.
Advances in protein chemistry and structural biology 2011;85():183-215.
2010: Tim Meyer; Marco D'Abramo; Adam Hospital; Manuel Rueda; Carles Ferrer-Costa; Alberto Pérez; Oliver Carrillo; Jordi Camps; Carles Fenollosa; Dmitry Repchevsky; Josep Lluis Gelpí; Modesto Orozco
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.
Structure (London, England : 1993) 2010;18(11):1399-409.
2010: 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.
Journal of computer-aided molecular design 2010;24(4):281-91.
2010: Jonathan K Watts; Nerea Martín-Pintado; Irene Gómez-Pinto; Jeremy Schwartzentruber; Guillem Portella; Modesto Orozco; Carlos González; Masad J Damha
Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility.
Nucleic acids research 2010;38(7):2498-511.
2010: Agustí Emperador; Tim Meyer; Modesto Orozco
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.
Proteins 2010;78(1):83-94.
2009: Alvaro Vázquez-Mayagoitia; Oscar Huertas; Giorgia Brancolini; Agostino Migliore; Bobby G Sumpter; Modesto Orozco; F Javier Luque; Rosa Di Felice; Miguel Fuentes-Cabrera
Ab initio study of the structural, tautomeric, pairing, and electronic properties of seleno-derivatives of thymine.
The journal of physical chemistry. B 2009;113(43):14465-72.
2009: Ignacio Faustino; Anna Aviño; Ivan Marchán; F Javier Luque; Ramon Eritja; Modesto Orozco
Unique tautomeric and recognition properties of thioketothymines?
Journal of the American Chemical Society 2009;131(35):12845-53.
2009: Hisao Saneyoshi; Stefania Mazzini; Anna Aviñó; Guillem Portella; Carlos González; Modesto Orozco; Victor E Marquez; Ramon Eritja
Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer.
Nucleic acids research 2009;37(17):5589-601.
2009: Ignacio Soteras; Flavio Forti; Modesto Orozco; F Javier Luque
Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies.
The journal of physical chemistry. B 2009;113(27):9330-4.
2009: Jordi Camps; Oliver Carrillo; Agustí Emperador; Laura Orellana; Adam Hospital; Manuel Rueda; Damjan Cicin-Sain; Marco D'Abramo; Josep Lluís Gelpí; Modesto Orozco
FlexServ: an integrated tool for the analysis of protein flexibility.
Bioinformatics (Oxford, England) 2009;25(13):1709-10.
2009: Tim Meyer; Xavier de la Cruz; Modesto Orozco
An atomistic view to the gas phase proteome.
Structure (London, England : 1993) 2009;17(1):88-95.
2009: Hisao Saneyoshi; Stefania Mazzini; Anna Aviñó; Guillem Portella; Carlos González; Modesto Orozco; Victor E Marquez; Ramon Eritja
The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamer.
Nucleic acids symposium series (2004) 2009;(53):109-10.
2008: Ignacio Soteras; Oscar Lozano; Carmen Escolano; Modesto Orozco; Mercedes Amat; Joan Bosch; F Javier Luque
Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams.
The Journal of organic chemistry 2008;73(19):7756-63.
2008: J Ramon Goñi; Carlos Fenollosa; Alberto Pérez; David Torrents; Modesto Orozco
DNAlive: a tool for the physical analysis of DNA at the genomic scale.
Bioinformatics (Oxford, England) 2008;24(15):1731-2.
2008: Julien Gros; Anna Aviñó; Jaime Lopez de la Osa; Carlos González; Laurent Lacroix; Alberto Pérez; Modesto Orozco; Ramon Eritja; Jean-Louis Mergny
8-Amino guanine accelerates tetramolecular G-quadruplex formation.
Chemical communications (Cambridge, England) 2008;(25):2926-8.
2008: Ignacio Soteras; Modesto Orozco; F Javier Luque
Induction effects in metal cation-benzene complexes.
Physical chemistry chemical physics : PCCP 2008;10(19):2616-24.
2008: Modesto Orozco; Agnes Noy; Alberto Pérez
Recent advances in the study of nucleic acid flexibility by molecular dynamics.
Current opinion in structural biology 2008;18(2):185-93.
2008: Alberto Pérez; Filip Lankas; F Javier Luque; Modesto Orozco
Towards a molecular dynamics consensus view of B-DNA flexibility.
Nucleic acids research 2008;36(7):2379-94.
2008: Flavio Forti; Xavier Barril; F Javier Luque; Modesto Orozco
Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian.
Journal of computational chemistry 2008;29(4):578-87.
2008: Alvaro Vazquez-Mayagoita; Oscar Huertas; Miguel Fuentes-Cabrera; Bobby G Sumpter; Modesto Orozco; F Javier Luque
Ab initio study of naphtho-homologated DNA bases.
The journal of physical chemistry. B 2008;112(7):2179-86.
2007: Joana Fort; Laura R de la Ballina; Hans E Burghardt; Carles Ferrer-Costa; Javier Turnay; Cristina Ferrer-Orta; Isabel Usón; Antonio Zorzano; Juan Fernandez-Recio; Modesto Orozco; M Antonia Lizarbe; Ignacio Fita; Manuel Palacín
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane.
The Journal of biological chemistry 2007;282(43):31444-52.
2007: José-Antonio Ortega; José Ramón Blas; Modesto Orozco; Anna Grandas; Enrique Pedroso; Jordi Robles
Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent.
Organic letters 2007;9(22):4503-6.
2007: Alberto Pérez; Iván Marchán; Daniel Svozil; Jirí Sponer; Thomas E Cheatham; Charles A Laughton; Modesto Orozco
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.
Biophysical journal 2007;92(11):3817-29.
2007: Manuel Rueda; Pablo Chacon; Modesto Orozco
Thorough validation of protein normal mode analysis: a comparative study with essential dynamics.
Structure (London, England : 1993) 2007;15(5):565-75.
2007: David Talavera; Christine Vogel; Modesto Orozco; Sarah A Teichmann; Xavier de la Cruz
The (in)dependence of alternative splicing and gene duplication.
PLoS computational biology 2007;3(3):e33.
2007: Jordi Muñoz-Muriedas; Xavier Barril; José María López; Modesto Orozco; F Javier Luque
A hydrophobic similarity analysis of solvation effects on nucleic acid bases.
Journal of molecular modeling 2007;13(2):357-65.
2007: Robert Soliva; Josep Lluis Gelpí; Carmen Almansa; Marina Virgili; Modesto Orozco
Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family.
Journal of medicinal chemistry 2007;50(2):283-93.
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.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(3):796-801.
2007: Carles Ferrer-Costa; Modesto Orozco; Xavier de la Cruz
Characterization of compensated mutations in terms of structural and physico-chemical properties.
Journal of molecular biology 2007;365(1):249-56.
2007: Anna Aviñó; Marta G Grimau; Margarita Alvira; Ramon Eritja; Raimundo Gargallo; Modesto Orozco; Carlos González
Triplex formation using oligonucleotide clamps carrying 8-aminopurines.
Nucleosides, nucleotides & nucleic acids 2007;26(8-9):979-83.
2007: David Talavera; Adam Hospital; Modesto Orozco; Xavier de la Cruz
A procedure for identifying homologous alternative splicing events.
BMC bioinformatics 2007;8():260.
2007: Agnes Noy; Alberto Pérez; Charles A Laughton; Modesto Orozco
Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water.
Nucleic acids research 2007;35(10):3330-8.
2007: José Ramón Blas; Jose Maria López-Bes; Manuel Márquez; Jonathan L Sessler; F Javier Luque; Modesto Orozco
Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution.
Chemistry (Weinheim an der Bergstrasse, Germany) 2007;13(4):1108-16.
2006: 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.
Journal of computational chemistry 2006;27(15):1769-80.
2006: Oscar Huertas; Jordi Poater; Miguel Fuentes-Cabrera; Modesto Orozco; Miquel Solà; F Javier Luque
Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives.
The journal of physical chemistry. A 2006;110(44):12249-58.
2006: David Talavera; Antonio Morreale; Tim Meyer; Adam Hospital; Carles Ferrer-Costa; Josep Lluis Gelpi; Xavier de la Cruz; Robert Soliva; F Javier Luque; Modesto Orozco
A fast method for the determination of fractional contributions to solvation in proteins.
Protein science : a publication of the Protein Society 2006;15(11):2525-33.
2006: Axel Bidon-Chanal; Marcelo A Martí; Alejandro Crespo; Mario Milani; Modesto Orozco; Martino Bolognesi; F Javier Luque; Darío A Estrin
Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N.
Proteins 2006;64(2):457-64.
2006: Ignacio Soteras; Oscar Lozano; Arantxa Gómez-Esqué; Carmen Escolano; Modesto Orozco; Mercedes Amat; Joan Bosch; F Javier Luque
On the origin of the stereoselectivity in the alkylation of oxazolopiperidone enolates.
Journal of the American Chemical Society 2006;128(20):6581-8.
2006: Manuel Rueda; F Javier Luque; Modesto Orozco
G-quadruplexes can maintain their structure in the gas phase.
Journal of the American Chemical Society 2006;128(11):3608-19.
2006: Agnes Noy; Tim Meyer; Manuel Rueda; Carles Ferrer; Antonion Valencia; Alberto Pérez; Xavier de la Cruz; J M López-Bes; SOLE POUPLANA; Juan Fernandez-Recio; F Javier Luque; Modesto Orozco
Data mining of molecular dynamics trajectories of nucleic acids.
Journal of biomolecular structure & dynamics 2006;23(4):447-56.
2006: Elena Cubero; F Javier Luque; Modesto Orozco
Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.
Biophysical journal 2006;90(3):1000-8.
2006: Oscar Huertas; José Ramón Blas; Ignacio Soteras; Modesto Orozco; F Javier Luque
Benzoderivatives of nucleic acid bases as modified DNA building blocks.
The journal of physical chemistry. A 2006;110(2):510-8.
2006: Josep Ramon Goñi; Juan M Vaquerizas; Joaquín Dopazo; Modesto Orozco
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.
BMC genomics 2006;7():63.
2006: Jaime López de la Osa; Carlos González; Raimundo Gargallo; Manuel Rueda; Elena Cubero; Modesto Orozco; Anna Aviñó; Ramon Eritja
Destabilization of quadruplex DNA by 8-aminoguanine.
Chembiochem : a European journal of chemical biology 2006;7(1):46-8.
2005: D Alonso; Isabel Dorronsoro; Laura Rubio; P Muñoz; Esther García-Palomero; M Del Monte; Axel Bidon-Chanal; Modesto Orozco; F Javier Luque; Ana Castro; Miguel Medina; Ana Martínez
Donepezil-tacrine hybrid related derivatives as new dual binding site inhibitors of AChE.
Bioorganic & medicinal chemistry 2005;13(24):6588-97.
2005: Carles Ferrer-Costa; Modesto Orozco; Xavier de la Cruz
Use of bioinformatics tools for the annotation of disease-associated mutations in animal models.
Proteins 2005;61(4):878-87.
2005: Pilar Muñoz-Ruiz; Laura Rubio; Esther García-Palomero; Isabel Dorronsoro; María del Monte-Millán; Rita Valenzuela; Paola Usán; Celia de Austria; Manuela Bartolini; Vincenza Andrisano; Axel Bidon-Chanal; Modesto Orozco; F Javier Luque; Miguel Medina; Ana Martínez
Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer's disease.
Journal of medicinal chemistry 2005;48(23):7223-33.
2005: Manuel Rueda; F Javier Luque; Modesto Orozco
Nature of minor-groove binders-DNA complexes in the gas phase.
Journal of the American Chemical Society 2005;127(33):11690-8.
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.
Bioinformatics (Oxford, England) 2005;21(14):3176-8.
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 research 2005;33(Web Server issue):W501-5.
2005: 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.
Journal of computer-aided molecular design 2005;19(6):401-19.
2005: Agnes Noy; Alberto Pérez; Manuel Márquez; F Javier Luque; Modesto Orozco
Structure, recognition properties, and flexibility of the DNA.RNA hybrid.
Journal of the American Chemical Society 2005;127(13):4910-20.
2005: Alejandro Crespo; Marcelo A Martí; Susana G Kalko; Antonio Morreale; Modesto Orozco; Jose L Gelpi; F Javier Luque; Darío A Estrin
Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism.
Journal of the American Chemical Society 2005;127(12):4433-44.
2005: Carles Curutchet; Axel Bidon-Chanal; Ignacio Soteras; Modesto Orozco; F Javier Luque
MST continuum study of the hydration free energies of monovalent ionic species.
The journal of physical chemistry. B 2005;109(8):3565-74.
2005: Antonio Morreale; Xavier de la Cruz; Tim Meyer; Josep Lluis Gelpí; F Javier Luque; Modesto Orozco
Partition of protein solvation into group contributions from molecular dynamics simulations.
Proteins 2005;58(1):101-9.
2004: Carles Ferrer-Costa; Modesto Orozco; Xavier de la Cruz
Sequence-based prediction of pathological mutations.
Proteins 2004;57(4):811-9.
2004: Antonio Morreale; Xavier de la Cruz; Tim Meyer; Josep Lluis Gelpí; F Javier Luque; Modesto Orozco
Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
Proteins 2004;57(3):458-67.
2004: Agnes Noy; Alberto Pérez; Filip Lankas; F Javier Luque; Modesto Orozco
Relative flexibility of DNA and RNA: a molecular dynamics study.
Journal of molecular biology 2004;343(3):627-38.
2004: Luc Marti; Anna Abella; Xavier de la Cruz; Silvia García-Vicente; Mercedes Unzeta; Christian Carpéné; Manuel Palacín; Xavier Testar; Modesto Orozco; Antonio Zorzano
Exploring the binding mode of semicarbazide-sensitive amine oxidase/VAP-1: identification of novel substrates with insulin-like activity.
Journal of medicinal chemistry 2004;47(20):4865-74.
2004: Manuel Rueda; Elena Cubero; Charles A Laughton; Modesto Orozco
Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?
Biophysical journal 2004;87(2):800-11.
2004: Irene Gómez-Pinto; Elena Cubero; Susana G Kalko; Vania Monaco; Gijsbert A van der Marel; Jacques H van Boom; Modesto Orozco; Carlos González
Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct.
The Journal of biological chemistry 2004;279(23):24552-60.
2004: Raúl Estévez; Michael Pusch; Carles Ferrer-Costa; Modesto Orozco; Thomas J Jentsch
Functional and structural conservation of CBS domains from CLC chloride channels.
The Journal of physiology 2004;557(Pt 2):363-78.
2004: José L Marco; Cristóbal de los Ríos; Antonio G García; Mercedes Villarroya; Maria Carreiras; Carla Martins; Ana Eleutério; Antonio Morreale; Modesto Orozco; F Javier Luque
Synthesis, biological evaluation and molecular modelling of diversely functionalized heterocyclic derivatives as inhibitors of acetylcholinesterase/butyrylcholinesterase and modulators of Ca2+ channels and nicotinic receptors.
Bioorganic & medicinal chemistry 2004;12(9):2199-218.
2004: José Ramón Blas; F Javier Luque; Modesto Orozco
Unique tautomeric properties of isoguanine.
Journal of the American Chemical Society 2004;126(1):154-64.
2004: Abel Valenzuela; David Talavera; Modesto Orozco; Xavier de la Cruz
Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species.
Journal of molecular biology 2004;335(2):495-502.
2004: Alberto Pérez; Agnes Noy; Filip Lankas; F Javier Luque; Modesto Orozco
The relative flexibility of B-DNA and A-RNA duplexes: database analysis.
Nucleic acids research 2004;32(20):6144-51.
2004: Jordi Muñoz-Muriedas; J M Lopez; Modesto Orozco; F Javier Luque
Molecular modelling approaches to the design of acetylcholinesterase inhibitors: new challenges for the treatment of Alzheimer's disease.
Current pharmaceutical design 2004;10(25):3131-40.
2004: J Ramon Goñi; Xavier de la Cruz; Modesto Orozco
Triplex-forming oligonucleotide target sequences in the human genome.
Nucleic acids research 2004;32(1):354-60.
2003: Anna Aviñó; Elena Cubero; Carlos González; Ramon Eritja; Modesto Orozco
Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives.
Journal of the American Chemical Society 2003;125(51):16127-38.
2003: Elena Cubero; Nicola G A Abrescia; Juan A Subirana; F Javier Luque; Modesto Orozco
Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.
Journal of the American Chemical Society 2003;125(47):14603-12.
2003: Modesto Orozco; Alberto Pérez; Agnes Noy; F Javier Luque
Theoretical methods for the simulation of nucleic acids.
Chemical Society reviews 2003;32(6):350-64.
2003: Antonio Morreale; Josep Lluis Gelpí; F Javier Luque; Modesto Orozco
Continuum and discrete calculation of fractional contributions to solvation free energy.
Journal of computational chemistry 2003;24(13):1610-23.
2003: Carles Curutchet; Josep M Bofill; Begoña Hernández; Modesto Orozco; F Javier Luque
Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations.
Journal of computational chemistry 2003;24(10):1263-75.
2003: Manuel Rueda; Susana G Kalko; F Javier Luque; Modesto Orozco
The structure and dynamics of DNA in the gas phase.
Journal of the American Chemical Society 2003;125(26):8007-14.
2003: Xavier Fradera; Manuel Márquez; Bradley D Smith; Modesto Orozco; F Javier Luque
Molecular dynamics study of 2rotaxanes: influence of solvation and cation on co-conformation.
The Journal of organic chemistry 2003;68(12):4663-73.
2003: Núria Escaja; Josep Lluis Gelpí; Modesto Orozco; Manuel Rico; Enrique Pedroso; Carlos González
Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad.
Journal of the American Chemical Society 2003;125(19):5654-62.
2003: Anna Aviñó; Miriam Frieden; Juan Carlos Morales; Beatriz G de la Torre; Ramón Güimil García; Modesto Orozco; Carlos González; Ramon Eritja
Properties of triple helices formed by oligonucleotides containing 8-aminopurines.
Nucleosides, nucleotides & nucleic acids 2003;22(5-8):645-8.
2003: Robert Soliva; Carmen Almansa; Susana G Kalko; F Javier Luque; Modesto Orozco
Theoretical studies on the inhibition mechanism of cyclooxygenase-2. Is there a unique recognition site?
Journal of medicinal chemistry 2003;46(8):1372-82.
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.
Journal of computational chemistry 2003;24(3):284-97.
2003: Carles Curutchet; A Salichs; Xavier Barril; Modesto Orozco; F Javier Luque
Transferability of fragmental contributions to the octanol/water partition coefficient: an NDDO-based MST study.
Journal of computational chemistry 2003;24(1):32-45.
2002: José Ramón Blas; Manuel Márquez; Jonathan L Sessler; F Javier Luque; Modesto Orozco
Theoretical study of anion binding to calix[4]pyrrole: the effects of solvent, fluorine substitution, cosolute, and water traces.
Journal of the American Chemical Society 2002;124(43):12796-805.
2002: Jordi Ribas; Elena Cubero; F Javier Luque; Modesto Orozco
Theoretical study of alkyl-pi and aryl-pi interactions. Reconciling theory and experiment.
The Journal of organic chemistry 2002;67(20):7057-65.
2002: Albert Salichs; M López; Victor Segarra; Modesto Orozco; F Javier Luque
Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study.
Journal of computer-aided molecular design 2002;16(8-9):569-83.
2002: Xavier Fradera; Xavier de la Cruz; Carlos H T P Silva; Josep Lluis Gelpí; F Javier Luque; Modesto Orozco
Ligand-induced changes in the binding sites of proteins.
Bioinformatics (Oxford, England) 2002;18(7):939-48.
2002: Anna Aviñó; Miriam Frieden; Juan Carlos Morales; Beatriz García de la Torre; Ramón Güimil García; Fernando Azorín; José Luis Gelpí; Modesto Orozco; Carlos González; Ramon Eritja
Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines.
Nucleic acids research 2002;30(12):2609-19.
2002: J Muñoz; Xavier Barril; B Hernández; Modesto Orozco; F Javier Luque
Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index.
Journal of computational chemistry 2002;23(5):554-63.
2002: Elena Cubero; Anna Aviñó; Beatriz G de la Torre; Miriam Frieden; Ramon Eritja; F Javier Luque; Carlos González; Modesto Orozco
Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives.
Journal of the American Chemical Society 2002;124(12):3133-42.
2002: Hay Dvir; Dawn M Wong; Michal Harel; Xavier Barril; Modesto Orozco; F Javier Luque; Diego Muñoz-Torrero; Pelayo Camps; Terrone L Rosenberry; Israel Silman; Joel Sussman
3D structure of Torpedo californica acetylcholinesterase complexed with huprine X at 2.1 A resolution: kinetic and molecular dynamic correlates.
Biochemistry 2002;41(9):2970-81.
2002: Xavier Barril; Susana G Kalko; Modesto Orozco; F Javier Luque
Rational design of reversible acetylcholinesterase inhibitors.
Mini reviews in medicinal chemistry 2002;2(1):27-36.
2002: Carles Ferrer-Costa; Modesto Orozco; Xavier de la Cruz
Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties.
Journal of molecular biology 2002;315(4):771-86.
2001: Pelayo Camps; Elena Gómez; Diego Muñoz-Torrero; Albert Badia; Nuria M Vivas; Xavier Barril; Modesto Orozco; F Javier Luque
Synthesis, in vitro pharmacology, and molecular modeling of syn-huprines as acetylcholinesterase inhibitors.
Journal of medicinal chemistry 2001;44(26):4733-6.
2001: Elena Cubero; F Javier Luque; Modesto Orozco
Theoretical studies of d(A:T)-based parallel-stranded DNA duplexes.
Journal of the American Chemical Society 2001;123(48):12018-25.
2001: Josep Lluis Gelpí; Susana G Kalko; Xavier Barril; Jordi Cirera; Xavier de la Cruz; F Javier Luque; Modesto Orozco
Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins.
Proteins 2001;45(4):428-37.
2001: Susana G Kalko; Josep Lluis Gelpí; Ignacio Fita; Modesto Orozco
Theoretical study of the mechanisms of substrate recognition by catalase.
Journal of the American Chemical Society 2001;123(39):9665-72.
2001: Xavier Barril; Modesto Orozco; F Javier Luque
Towards improved acetylcholinesterase inhibitors: a structural and computational approach.
Mini reviews in medicinal chemistry 2001;1(3):255-66.
2001: Robert Soliva; Vania Monaco; Irene Gómez-Pinto; Nico J Meeuwenoord; G A Marel; J H Boom; Carlos González; Modesto Orozco
Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety.
Nucleic acids research 2001;29(14):2973-85.
2001: Anna Aviñó; Juan Carlos Morales; Miriam Frieden; Beatriz G de la Torre; Ramon Güimil García; Elena Cubero; F Javier Luque; Modesto Orozco; Fernando Azorín; Ramon Eritja
Parallel-stranded hairpins containing 8-aminopurines. Novel efficient probes for triple-helix formation.
Bioorganic & medicinal chemistry letters 2001;11(13):1761-3.
2001: Elena Cubero; Ramón Güimil García; F Javier Luque; Ramon Eritja; Modesto Orozco
The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine.
Nucleic acids research 2001;29(12):2522-34.
2001: Manuel Rueda; F Javier Luque; Modesto Orozco
A theoretical investigation on the effect of remote amino groups in hydrogen bonding of nucleic acids.
Biopolymers 2001;61(1):52-60.
2000: B Hernández; Robert Soliva; F Javier Luque; Modesto Orozco
Misincorporation of 2'-deoxyoxanosine into DNA: a molecular basis for NO-induced mutagenesis derived from theoretical calculations.
Nucleic acids research 2000;28(24):4873-83.
2000: Pelayo Camps; J Morral; Diego Muñoz-Torrero; Albert Badia; Josep-E Baños; Nuria M Vivas; Xavier Barril; Modesto Orozco; F Javier Luque
New tacrine-huperzine A hybrids (huprines): highly potent tight-binding acetylcholinesterase inhibitors of interest for the treatment of Alzheimer's disease.
Journal of medicinal chemistry 2000;43(24):4657-66.
2000: Robert Soliva; Ramón Güimil García; José Ramón Blas; Ramon Eritja; J L Asensio; Carlos González; F Javier Luque; Modesto Orozco
DNA-triplex stabilizing properties of 8-aminoguanine.
Nucleic acids research 2000;28(22):4531-9.
2000: Mercedes Amat; Joan Bosch; J Hidalgo; Margalida Cantó; Maria Pérez; Núria Llor; Elies Molins; Carlos Miravitlles; Modesto Orozco; J Luque
Synthesis of enantiopure trans-3,4-disubstituted piperidines. An enantiodivergent synthesis of (+)- and (-)-paroxetine.
The Journal of organic chemistry 2000;65(10):3074-84.
2000: B Hernández; F Javier Luque; Modesto Orozco
Mixed QM/MM molecular electrostatic potentials.
Journal of computer-aided molecular design 2000;14(4):329-39.
1999: Xavier Barril; Modesto Orozco; F Javier Luque
Predicting relative binding free energies of tacrine-huperzine A hybrids as inhibitors of acetylcholinesterase.
Journal of medicinal chemistry 1999;42(25):5110-9.
1999: Pelayo Camps; R El Achab; D M Görbig; J Morral; Diego Muñoz-Torrero; Albert Badia; J Eladi Baños; Nuria M Vivas; Xavier Barril; Modesto Orozco; F Javier Luque
Synthesis, in vitro pharmacology, and molecular modeling of very potent tacrine-huperzine A hybrids as acetylcholinesterase inhibitors of potential interest for the treatment of Alzheimer's disease.
Journal of medicinal chemistry 1999;42(17):3227-42.
1999: Robert Soliva; F Javier Luque; C Alhambra; Modesto Orozco
Role of sugar re-puckering in the transition of A and B forms of DNA in solution. A molecular dynamics study.
Journal of biomolecular structure & dynamics 1999;17(1):89-99.
1999: Robert Soliva; F Javier Luque; Modesto Orozco
Can G-C Hoogsteen-wobble pairs contribute to the stability of d(G. C-C) triplexes?
Nucleic acids research 1999;27(11):2248-55.
1999: Ramon Güimil García; E Ferrer; M J Macías; Ramon Eritja; Modesto Orozco
Theoretical calculations, synthesis and base pairing properties of oligonucleotides containing 8-amino-2'-deoxyadenosine.
Nucleic acids research 1999;27(9):1991-8.
1999: F Javier Luque; Xavier Barril; Modesto Orozco
Fractional description of free energies of solvation.
Journal of computer-aided molecular design 1999;13(2):139-52.
1998: Ramón Güimil García; A Bachi; Ramon Eritja; F Javier Luque; Modesto Orozco
Triple helix stabilization properties of oligonucleotides containing 8-amino-2'-deoxyguanosine.
Bioorganic & medicinal chemistry letters 1998;8(21):3011-6.
1998: E Jiménez-García; Alejandro Vaquero; M Lluïsa Espinás; R Soliva; Modesto Orozco; Jordi Bernués; Fernando Azorín
The GAGA factor of Drosophila binds triple-stranded DNA.
The Journal of biological chemistry 1998;273(38):24640-8.
1998: Xavier Barril; Carlos Alemán; Modesto Orozco; F Javier Luque
Salt bridge interactions: stability of the ionic and neutral complexes in the gas phase, in solution, and in proteins.
Proteins 1998;32(1):67-79.
1998: Elena Cubero; F Javier Luque; Modesto Orozco
Is polarization important in cation-pi interactions?
Proceedings of the National Academy of Sciences of the United States of America 1998;95(11):5976-80.
1997: Modesto Orozco; C Vega; A Parraga; I García-Sáez; Miquel Coll; S Walsh; Timothy J Mantle; F Javier Luque
On the reaction mechanism of class Pi glutathione S-transferase.
Proteins 1997;28(4):530-42.
1997: B Hernández; Modesto Orozco; F Javier Luque
Role of tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase.
Journal of computer-aided molecular design 1997;11(2):153-62.
1997: Modesto Orozco; F Javier Luque
Computer-assisted drug design: current status and future trends.
Methods and findings in experimental and clinical pharmacology 1997;19 Suppl A():33-5.
1996: B Hernández; Modesto Orozco; F Javier Luque
Tautomerism of xanthine and alloxanthine: a model for substrate recognition by xanthine oxidase.
Journal of computer-aided molecular design 1996;10(6):535-44.
1995: C Alhambra; F Javier Luque; J Portugal; Modesto Orozco
Molecular dynamics study of the binding of elsamicin A to DNA.
European journal of biochemistry / FEBS 1995;230(2):555-66.
1994: J Gallego; F Javier Luque; Modesto Orozco; Federico Gago
Binding of echinomycin to d(GCGC)2 and d(CCGG)2: distinct stacking interactions dictate the sequence-dependent formation of Hoogsteen base pairs.
Journal of biomolecular structure & dynamics 1994;12(1):111-29.
1994: J Gallego; F Javier Luque; Modesto Orozco; C Burgos; Julio Alvarez-Builla; M M Rodrigo; Federico Gago
DNA sequence-specific reading by echinomycin: role of hydrogen bonding and stacking interactions.
Journal of medicinal chemistry 1994;37(11):1602-9.
1992: A Párraga; Modesto Orozco; J Portugal
Experimental and modelling studies on the DNA cleavage by elsamicin A.
European journal of biochemistry / FEBS 1992;208(2):227-33.
1992: Carlos Alemán; Modesto Orozco
On the suitability of semiempirical calculations as sources of force field parameters.
Journal of computer-aided molecular design 1992;6(4):331-48.
1990: Modesto Orozco; F Javier Luque
A practical procedure for the determination of electrostatic charges of large molecules.
Journal of computer-aided molecular design 1990;4(4):411-26.
1990: Modesto Orozco; Enric Isidre Canela; R Franco
A quantum chemical study of the enzymatic deamination of benzoadenine derivatives. A theoretical model of the interactions occurring between nucleosides and the active site of adenosine deaminase.
European journal of biochemistry / FEBS 1990;188(1):155-63.
1990: Modesto Orozco; Carmen Lluis; Josefa Mallol; Enric Isidre Canela; Rafael Franco
Quantum chemical study of the electronic and conformational characteristics of adenosine and 8-substituted derivatives: functional implications in the mechanism of reaction of adenosine deaminase.
Journal of pharmaceutical sciences 1990;79(2):133-7.
1989: Modesto Orozco; F Javier Luque
POEAMS: program for outliers elimination in 'anomalous' multidimensional space.
Computer applications in the biosciences : CABIOS 1989;5(3):241-2.
1989: Modesto Orozco; R Franco
TEFOOL/2: a program for theoretical drug design on microcomputers.
Computer applications in the biosciences : CABIOS 1989;5(3):219-26.
1989: Modesto Orozco; Enric Isidre Canela; Rafael Franco
Theoretical study of the protonation and tautomerization of adenosine, formycin, and their 2-NH2 and 2-F derivatives: functional implications in the mechanism of reaction of adenosine deaminase.
Molecular pharmacology 1989;35(2):257-64.
1989: Modesto Orozco; Enric Isidre Canela; Carmen Lluis; Josefa Mallol; Rafael Franco
Theoretical study of the tautomerism of adenosine and formycin: functional implications.
Progress in clinical and biological research 1989;291():365-8.
1988: Modesto Orozco; F Javier Luque
POEMS: program for outliers elimination in multidimensional space.
Computer applications in the biosciences : CABIOS 1988;4(3):381-5.