Publications

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P. Sfriso, Emperador, A., Orellana, L., Hospital, A., Gelpí, J. L., and Orozco, M., Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations, Journal of Chemical Theory and Computation, vol. 8. pp. 4707-4718, 2012.
J. Camps, Carrillo, O., Emperador, A., Orellana, L., Hospital, A., Rueda, M., Cicin, D., D'Abramo, M., Gelpí, J. L., and Orozco, M., FlexServ: An integrated tool for the analysis of protein flexibility. Bioinformatics (2009) 25 (13): 1709-1710, 2009.
A. Pérez, Luque, F. J., and Orozco, M., Frontiers in Molecular Dynamics Simulations of DNA., Accounts of chemical research. 2012.
M. Terrazas, Alagia, A., Faustino, I., Orozco, M., and Eritja, R., Functionalization of the 3'-ends of DNA and RNA strands with N-ethyl-N-coupled nucleosides: a promising approach to avoid 3'-exonuclease-catalyzed hydrolysis of therapeutic oligonucleotides., Chembiochem : a European journal of chemical biology, vol. 14, no. 4. pp. 510-20, 2013.
O. Flores, Deniz, O., Soler-López, M., and Orozco, M., Fuzziness and noise in nucleosomal architecture., Nucleic Acids Res, vol. 42, no. 8. pp. 4934-46, 2014.
M. Rueda, Luque, F. J., and Orozco, M., G-DNA can maintain its structure in the gas phase. J. Am. Chem. Soc., 2006.
E. M. Novoa, Castro, M., Orozco, M., and de Pouplana., L. R., A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins. FEBS Lett., (2010), 584, 460-466., 2009.
D. Svozil, Marchán, I., Pérez, A., Cheatham, T. E., Forti, F., Luque, F. J., Orozco, M., and Sponer, J., Geometrical and Electronic Structure Variability of the Sugar-phosphate Backbone in Nucleic Acids. J. Phys. Chem. B, 112 (27), pp 8188?8197, 2008.
N. Utz, Meyer, T., Rink, G., Orozco, M., and Koslowski, T., Geometry, Dynamics, and Electronic Structure of DNA–Carbon Nanotube Hybrids, J. Phys. Chem. C, vol. 116 (20), pp 11278–11282. 2012.
O. Carrillo and Orozco, M., GRID-based molecular dynamics. A Tool for genomic-scale simulations of channels in proteins. Proteins. 70, 892-899, 2008.
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.
M. V. Georgieva, Yahya, G., Codó, L., Ortiz, R., Teixidó, L., Claros, J., Jara, R., Jara, M., Iborra, A., Gelpí, J. L., Gallego, C., Orozco, M., and Aldea, M., Inntags: small self-structured epitopes for innocuous protein tagging., Nat Methods. 2015.
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., J Am Chem Soc, vol. 136, no. 8. pp. 3075-86, 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., 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.
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.
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.
A. Hospital, Goñi, J. Ramon, Orozco, M., and Gelpí, J. L., Molecular dynamics simulations: advances and applications., Adv Appl Bioinform Chem, vol. 10. pp. 37-47, 2015.
M. Barbany, Meyer, T., Hospital, A., Faustino, I., D'Abramo, M., Morata, J., Orozco, M., and de la Cruz, X., Molecular dynamics study of naturally existing cavity couplings in proteins., PLoS One, vol. 10, no. 3. p. e0119978, 2015.
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.
M. A. Sáez, Fernández-Rodríguez, J., Moutinho, C., Sánchez-Mut, J. V., Gomez, A., Vidal, E., Petazzi, P., Szczesna, K., Lopez-Serra, P., Lucariello, M., Lorden, P., Delgado-Morales, R., de la Caridad, O. J., Huertas, D., Gelpí, J. L., Orozco, M., López-Doriga, A., Milà, M., Perez-Jurado, L. A., Pineda, M., Armstrong, J., Lázaro, C., and Esteller, M., Mutations in JMJD1C are involved in Rett syndrome and intellectual disability., Genet Med. 2015.
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 Res, vol. 41, no. Web Server issue. pp. W47-55, 2013.
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.
X. S. Puente, Beà, S., Valdés-Mas, R., Villamor, N., Gutiérrez-Abril, J., Martín-Subero, J. I., Munar, M., Rubio-Pérez, C., Jares, P., Aymerich, M., Baumann, T., Beekman, R., Belver, L., Carrió, A., Castellano, G., Clot, G., Colado, E., Colomer, D., Costa, D., Delgado, J., Enjuanes, A., Estivill, X., Ferrando, A. A., Gelpí, J. L., González, B., González, S., González, M., Gut, M., Hernández-Rivas, J. M., López-Guerra, M., Martín-García, D., Navarro, A., Nicolás, P., Orozco, M., Payer, Á. R., Pinyol, M., Pisano, D. G., Puente, D. A., Queirós, A. C., Quesada, V., Romeo-Casabona, C. M., Royo, C., Royo, R., Rozman, M., Russiñol, N., Salaverria, I., Stamatopoulos, K., Stunnenberg, H. G., Tamborero, D., Terol, M. J., Valencia, A., López-Bigas, N., Torrents, D., Gut, I., López-Guillermo, A., López-Otín, C., and Campo, E., Non-coding recurrent mutations in chronic lymphocytic leukaemia., Nature. 2015.
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.

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