Publications

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M. Nadal-Ribelles, Conde, N., Flores, O., González-Vallinas, J., Eyras, E., Orozco, M., de Nadal, E., and Posas, F., Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling., Genome biology, vol. 13, no. 11. p. R106, 2012.
M. Nadal-Ribelles, Conde, N., Flores, O., González-Vallinas, J., Eyras, E., Orozco, M., de Nadal, E., and Posas, F., Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling., Genome biology, vol. 13, no. 11. p. R106, 2012.
J. Muñoz-Muriedas, Barril, X., López, J. M., Orozco, M., and Luque, F. J., A hydrophobic similarity analysis of solvation effects on nucleic acids. J.Mol.Mod, 2006.
A. Pérez, Castellazzi, C. L., Battistini, F., Collinet, K., Flores, O., Deniz, O., Ruiz, M. L., Torrents, D., Eritja, R., Soler-López, M., and Orozco, M., Impact of methylation on the physical properties of DNA., Biophysical journal, vol. 102, no. 9. pp. 2140-8, 2012.
A. Noy, Soteras, I., Luque, F. J., and Orozco, M., The impact of monovalent ion force-field model in nucleic acids simulations. Phys. Chem. Chem. Phys., 2009, 11, 10596-10607, 2009.
S. Sciabola, Cao, Q., Orozco, M., Faustino, I., and Stanton, R. V., Improved nucleic acid descriptors for siRNA efficacy prediction., Nucleic acids research, vol. 41, no. 3. pp. 1383-94, 2013.
D. Talavera, Vogel, C., Orozco, M., Teichmann, S. A., and de la Cruz, X., The (In)dependence of alternative splicing and gene duplication. PLOS Comp.Biol. 3, 375-388, 2007.
I. Soteras, Chipot, C., Orozco, M., and Luque, F. J., Induction effects in metal cation-benzene complexes. Phys.Chem.Chem.Phys, 10, 2616-2624, 2008.
A. Bidon-Chanal, Martí, M., Crespo, A., Milani, M., Orozco, M., Bolognesi, M., Luque, F. J., and Estrín, D. A., Ligand-induced dynamical regulation of NO conversion in Mycobacterium Tubercolisis truncated-hemoglobin-N. Proteins, 2006.
F. Raimondi, Felline, A., Portella, G., Orozco, M., and Fanelli, F., Light on the structural communication in Ras GTPases., Journal of biomolecular structure & dynamics, vol. 31, no. 2. pp. 142-57, 2013.
F. Raimondi, Felline, A., Portella, G., Orozco, M., and Fanelli, F., Light on the structural communication in Ras GTPases., Journal of biomolecular structure & dynamics, vol. 31, no. 2. pp. 142-57, 2013.
A. Morreale, de la Cruz, X., Meyer, T., Gelpí, J. L., Luque, F. J., and Orozco, M., Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?. Proteins, 2004.
O. Huertas, Poater, J., Fuentes-Cabrera, M., Orozco, M., Sola, M., and Luque, F. J., Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives. J.Phys.Chem.B, 2006.
G. Portella, Germann, M. W., Hud, N. V., and Orozco, M., MD and NMR Analyses of Choline and TMA Binding to Duplex DNA: On the Origins of Aberrant Sequence-Dependent Stability by Alkyl Cations in Aqueous and Water-Free Solvents., Journal of the American Chemical Society. 2014.
G. Portella, Germann, M. W., Hud, N. V., and Orozco, M., MD and NMR Analyses of Choline and TMA Binding to Duplex DNA: On the Origins of Aberrant Sequence-Dependent Stability by Alkyl Cations in Aqueous and Water-Free Solvents., Journal of the American Chemical Society. 2014.
A. Hospital, Andrio, P., Fenollosa, C., Cicin-Sain, D., Orozco, M., and Gelpí, J. L., MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations., Bioinformatics (Oxford, England), vol. 28, no. 9. pp. 1278-9, 2012.
T. Meyer, D'Abramo, M., Hospital, A., Rueda, M., Ferrer-Costa, C., Pérez, A., Carrillo, O., Camps, J., Fenollosa, C., Repchevsky, D., Gelpí, J. L., and Orozco, M., MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories., Structure (London, England : 1993), vol. 18, no. 11. pp. 1399-409, 2010.
T. Meyer, D'Abramo, M., Hospital, A., Rueda, M., Ferrer-Costa, C., Pérez, A., Carrillo, O., Fenollosa, C., Perchevsky, D., Gelpí, J. L., and Orozco, M., MoDEL (Molecular Dynamics Extended Library). A database of atomistic molecular dynamics simulations. Structure. (2010), 18, 1399-1409., 2010.
J. Muñoz-Muriedas, Perspicace, S., Bech, N., Guccione, S., Orozco, M., and Luque, F. J., Molecular Alignment Based on Hydrophobic Similarity as a Tool in Drug Design. J.Comput. Aided Mol. Design, 2005.
L. Kowalczyk, Ratera, M., Paladino, A., Bartoccioni, P., Errasti-Murugarren, E., Valencia, E., Portella, G., Bial, S., Zorzano, A., Fita, I., Orozco, M., Carpena, X., Vázquez-Ibar, J. L., and Palacín, M., Molecular basis of substrate-induced permeation by an amino acid antiporter., Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 10. pp. 3935-40, 2011.
C. Curutchet, Bidon-Chanal, A., Soteras, I., Orozco, M., and Luque, F. J., MST continuum study of the hydration free energies of monovalent ionic species. J.Phys.Chem., 2005.
F. Forti, Cavasotto, C. N., Orozco, M., Barril, X., and Luque, J. F., A Multilevel Strategy for the Exploration of the Conformational Flexibility of Small Molecules, J. Chem. Theory Comput, 8 (5), pp 1808–1819 vol. 2012.
G. Portella and Orozco, M., Multiple routes characterize the folding of a small DNA hairpin. Angew. Chem. Int. Ed. Eng. (2010), 49, 7673-7676., 2010.
A. Hospital, Faustino, I., Collepardo-Guevara, R., González, C., Gelpí, J. L., and Orozco, M., NAFlex: a web server for the study of nucleic acid flexibility., Nucleic acids research, vol. 41, no. Web Server issue. pp. W47-55, 2013.
A. N. Naganathan and Orozco, M., The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding., Journal of the American Chemical Society, vol. 133, no. 31. pp. 12154-61, 2011.
J. Sponer, Jurecka, P., Marchán, I., Luque, F. J., Orozco, M., and Hobza, P., Nature of base stacking. Reference quantum chemical stacking energies in ten unique B-DNA base pair steps. Chem.Eur.Journal, 2006.
M. D'Abramo, Castellazzi, C. L., Orozco, M., and Amadei, A., On the nature of DNA hyperchromic effect., The journal of physical chemistry. B, vol. 117, no. 29. pp. 8697-704, 2013.
M. Rueda, Luque, F. J., and Orozco, M., The nature of minor-groove binders-DNA complexes in the gas phase. J.Am.Chem.Soc., 2005.
C. Laughton and Orozco, M., Nucleic Acid Themed Issue. Editorial. Phys. Chem. Chem. Phys., 2009, 11, 10541-10542, 2009.
F. Raimondi, Portella, G., Orozco, M., and Fanelli, F., Nucleotide binding switches the information flow in ras GTPases., PLoS computational biology, vol. 7, no. 3. p. e1001098, 2011.
F. Raimondi, Portella, G., Orozco, M., and Fanelli, F., Nucleotide switches the information flow in Ras GTPases. In Press, 2011.
O. Flores and Orozco, M., nucleR: a package for non-parametric nucleosome positioning., Bioinformatics (Oxford, England), vol. 27, no. 15. pp. 2149-50, 2011.
I. Soteras, Lozano, O., Gomez-Esque, A., Escolano, C., Orozco, M., Amat, M., Bosch, J., and Luque, F. J., On the origin of the stereoselectivity in the alkylation of oxazolopiperidone enolates.. J Am Chem Soc., 2006.
A. Morreale, de la Cruz, X., Meyer, T., Gelpí, J. L., Luque, F. J., and Orozco, M., Partition of protein solvation into group contributions from molecular dynamics simulations. Proteins, 2005.
A. Klamt, Mennucci, B., Tomasi, J., Barone, V., Curutchet, C., Orozco, M., and Luque, F. J., On the performance of continuum solvation methods. A comment on Universal Approaches to Solvation Modeling. Acc. Chem. Res., 2009, 42 (4), pp 489?492, 2009.
P. Banás, Hollas, D., Zgarbová, M., Jurecka, P., Orozco, M., Cheatham, T. E., Sponer, J., and Otyepka, M., Performance of molecular mechanics force-fields for RNA simulations. Stability of UUCG and GNRA hairpins. J. Chem. Theory Comput., 2010, 6 (12), pp 3836?3849, 2010.
I. Soteras, Forti, F., Orozco, M., and Luque, F. J., Performance of the IEF-MST Solvation Continuum Model in a Blind Test Prediction of Hydration Free Energies. J. Phys. Chem. B, 2009, 113 (27), pp 9330?9334, 2009.
I. Soteras, Orozco, M., and Luque, F. J., Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. J.Computer Aided Mol.Design. (2010), 24, 281-291., 2010.
O. Deniz, Flores, O., Battistini, F., Pérez, A., Soler-López, M., and Orozco, M., Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast., BMC genomics, vol. 12. p. 489, 2011.
C. Ferrer-Costa, Gelpí, J. L., Zamakola, L., Parrága, I., de la Cruz, X., and Orozco, M., PMUT: A Web-based tool for the annotation of pathological mutations on proteins. Bioinformatics, 2005.
F. J. Luque, Dehez,, Chipot, C., and Orozco, M., Polarization effects in molecular interactions. Wiley Interdisciplinary Reviews: Computational Molecular Science, n/a., 2011.
D. Talavera, Hospital, A., Orozco, M., and de la Cruz, X., A Procedure for the identification of homologous alternative splicing events. BMC. Bioinformatics, 8, 260-271, 2007.
A. Emperador, Meyer, T., and Orozco, M., Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials. Proteins, 78, 83-94, 2009.
A. N. Naganathan and Orozco, M., The protein folding transition-state ensemble from a Gō-like model., Physical chemistry chemical physics : PCCP, vol. 13, no. 33. pp. 15166-74, 2011.
T. Meyer, Gabelica, V., Grubmüller, H., and Orozco, M., Proteins in the gas phase. WIRES Comput.Mol.Sci, 2013.
L. Conde, Vaquerizas, J. M., Ferrer-Costa, C., de la Cruz, X., Orozco, M., and Dopazo, J., PupasView: A visual tool for selecting suitable SNPs with putative pathological effects in genes for geotyping purporses. Nucleic Acid. Res., 2005.
A. Pérez, Marchán, I., Svozil, D., Sponer, J., Cheatham, T. E., Laughton, C., and Orozco, M., Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophysical Journal 92, 3817-3829, 2007.
C. Pons, Talavera, D., de la Cruz, X., Orozco, M., and Fernández-Recio, J., Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking., Journal of chemical information and modeling, vol. 51, no. 2. pp. 370-7, 2011.
E. Fadrná, Spacková, N., Sarzyñska, J., Koca, J., Orozco, M., Cheatham, T. E., and Sponer, J., Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields. J. Chem. Theory Comput., 2009, 5 (9), pp 2514?2530, 2009.
E. M. Novoa, de Pouplana, L. R., and Orozco, M., Small Molecule Docking from Theoretical Structural Models, Computational Modeling of Biological Systems Biological and Medical Physics, Biomedical Engineering. pp. 75-95 , 2012.

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