Publications

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2013
Martin-Pintado, N., Deleavey, G.F., Portella, G., Campos-Olivas, R., Orozco, M., Damha, M.J. & González, C. Backbone FCH⋅⋅⋅O Hydrogen Bonds in 2'F-Substituted Nucleic Acids. Angewandte Chemie (International ed. in English) (2013).doi:10.1002/anie.201305710
Rueda, M., Orozco, M., Totrov, M. & Abagyan, R. BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry. BMC structural biology 13, 32 (2013).
Gracia, E., Farré, D., Cortés, A., Ferrer-Costa, C., Orozco, M., Mallol, J., Lluís, C., Canela, E.I., McCormick, P.J., Franco, R., Fanelli, F. & Casadó, V. 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 27, 1048-61 (2013).
Islam, B., Sgobba, M., Laughton, C., Orozco, M., Sponer, J., Neidle, S. & Haider, S. Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. Nucleic acids research 41, 2723-35 (2013).
Naganathan, A.N. & Orozco, M. The conformational landscape of an intrinsically disordered DNA-binding domain of a transcription regulator. The journal of physical chemistry. B 117, 13842-50 (2013).
Jamroz, M., Orozco, M., Kolinski, A. & Kmiecik, S. Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field. (2013).
Orozco, M. Data deluge in genomics”. Roche-Instituto Principe Felipe meeting on “Sequencing in the clinical practices”. (2013).
Orozco, M. "DNA from the electron to the chromatinVIII", Biogune Anniversary Distinguished Lecture. (2013).
Orozco, M. “DNA simulation in the postgenomic era”. Plenary lecture. Department of Pharmacy. North Caroline State University. (2013).
Orozco, M. 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 10, 29-30; discussion 39-40 (2013).
Emperador, A., Solernou, A., Sfriso, P., Pons, C., Gelpí, J.L., Fernández-Recio, J. & Orozco, M. Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations. Journal of Chemical Theory and Computation 9, 1222–1229 (2013).
Orozco, M. “Expanding the frontiers of molecular dynamics simulations of DNA”. CECAM Conference. University of Vienna. (2013).
Sfriso, P., Hospital, A., Emperador, A. & Orozco, M. Exploration of conformational transition pathways from coarse-grained simulations. Bioinformatics (Oxford, England) 29, 1980-6 (2013).
Candotti, M., Pérez, A., Ferrer-Costa, C., Rueda, M., Meyer, T., Gelpí, J.L. & Orozco, M. Exploring early stages of the chemical unfolding of proteins at the proteome scale. PLoS computational biology 9, e1003393 (2013).
Orozco, M. “Exploring protein flexibility”. Plenary Lecture. Cambridge University. (2013).
Terrazas, M., Alagia, A., Faustino, I., Orozco, M. & 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 14, 510-20 (2013).
Sciabola, S., Cao, Q., Orozco, M., Faustino, I. & Stanton, R.V. Improved nucleic acid descriptors for siRNA efficacy prediction. Nucleic acids research 41, 1383-94 (2013).
Orozco, M. “In Silico Biology” Ciclo de Conferencias Montpelier. (2013).
Raimondi, F., Felline, A., Portella, G., Orozco, M. & Fanelli, F. Light on the structural communication in Ras GTPases. Journal of biomolecular structure & dynamics 31, 142-57 (2013).
Raimondi, F., Felline, A., Portella, G., Orozco, M. & Fanelli, F. Light on the structural communication in Ras GTPases. Journal of biomolecular structure & dynamics 31, 142-57 (2013).
Orozco, M. “The moleclar basis of the transport cycle of APC anti-porters”. Invited Talk. PRACE Scientific Conference. (2013).
Orozco, M. “Multilevel simulation of DNA”. Invited lecture. American Chemical Society Meeting. (2013).
Hospital, A., Faustino, I., Collepardo-Guevara, R., González, C., Gelpí, J.L. & Orozco, M. NAFlex: a web server for the study of nucleic acid flexibility. Nucleic acids research 41, W47-55 (2013).
D'Abramo, M., Castellazzi, C.L., Orozco, M. & Amadei, A. On the nature of DNA hyperchromic effect. The journal of physical chemistry. B 117, 8697-704 (2013).
Orozco, M. “New challenges in the representation of protein dynamics”. Plenary Lecture. Institute of Nanosciences. (2013).
Meyer, T., Gabelica, V., Grubmüller, H. & Orozco, M. Proteins in the gas phase. (2013).
Aviñó, A., Portella, G., Ferreira, R., Gargallo, R., Mazzini, S., Gabelica, V., Orozco, M. & Eritja, R. Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures. The FEBS journal (2013).doi:10.1111/febs.12670
Dršata, T., Pérez, A., Orozco, M., Morozov, A.V., Sponer, J. & Lankaš, F. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. Journal of chemical theory and computation 9, 707-721 (2013).
Candotti, M., Esteban-Martín, S., Salvatella, X. & Orozco, M. Toward an atomistic description of the urea-denatured state of proteins. Proceedings of the National Academy of Sciences of the United States of America 110, 5933-8 (2013).
Portella, G., Battistini, F. & Orozco, M. Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations. PLoS computational biology 9, e1003354 (2013).
Durán, E., Djebali, S., González, S., Flores, O., Mercader, J.M., Guigó, R., Torrents, D., Soler-López, M. & Orozco, M. Unravelling the hidden DNA structural/physical code provides novel insights on promoter location. Nucleic acids research 41, 7220-30 (2013).
Orozco, M. “When mass spectroscopy and molecular simulations meet”. Invited Talk. CECAM Meeting. Frontiers of Computational Biomolecular Spectroscopy and Mass Spectrometry. (2013).
Orozco, M. “When physics and biology meet. The 2013 Nobel Award of Chemistry”. Sant Albert Plenary Lecture. Physical Engineering Sant Albert Plenary Lecture. (2013).
2012
Chaudhuri, R., Laughton, C.A., Carrillo, O. & Orozco, M. Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design. J. Chem. Theory Comput. (2012).
Gracia, E., Farré, D., Cortés, A., Ferrer-Costa, C., Orozco, M., Mallol, J., Lluís, C., Canela, E.I., McCormick, P.J., Franco, R., Fanelli, F. & Casadó, V. 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 (2012).doi:10.1096/fj.12-212621
Barbany, M., Morata, J., Meyer, T., Lois, S., Orozco, M. & de la Cruz, X. Characterization of the impact of alternative splicing on protein dynamics: the cases of glutathione S-transferase and ectodysplasin-A isoforms. Proteins 80, 2235-49 (2012).
García-Fandiño, R., Bernadó, P., Ayuso-Tejedor, S., Sancho, J. & Orozco, M. Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case. PLoS computational biology 8, e1002647 (2012).
Orozco, M. 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 (2012).doi:10.1016/j.plrev.2012.10.010
Kulis, M., Heath, S., Bibikova, M., Queirós, A.C., Navarro, A., Clot, G., Martínez-Trillos, A., Castellano, G., Brun-Heath, I., Pinyol, M., Barberán-Soler, S., Papasaikas, P., Jares, P., Beà, S., Rico, D., Ecker, S., Rubio, M., Royo, R., Ho, V., Klotzle, B., Hernández, L., Conde, L., López-Guerra, M., Colomer, D., Villamor, N., Aymerich, M., Rozman, M., Bayés, M., Gut, M., Gelpí, J.L., Orozco, M., Fan, J.-B., Quesada, V., Puente, X.S., Pisano, D.G., Valencia, A., López-Guillermo, A., Gut, I., López-Otín, C., Campo, E. & Martín-Subero, J.I. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nature genetics 44, 1236-42 (2012).
Kulis, M., Heath, S., Bibikova, M., Queirós, A.C., Navarro, A., Clot, G., Martínez-Trillos, A., Castellano, G., Brun-Heath, I., Pinyol, M., Barberán-Soler, S., Papasaikas, P., Jares, P., Beà, S., Rico, D., Ecker, S., Rubio, M., Royo, R., Ho, V., Klotzle, B., Hernández, L., Conde, L., López-Guerra, M., Colomer, D., Villamor, N., Aymerich, M., Rozman, M., Bayes, M., Gut, M., Gelpí, J.L., Orozco, M., Fan, J.-B., Quesada, V., Puente, X.S., Pisano, D.G., Valencia, A., López-Guillermo, A., Gut, I., López-Otín, C., Campo, E. & Martín-Subero, J.I. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nature genetics 44, 1236-42 (2012).
Djebali, S., Lagarde, J., Kapranov, P., Lacroix, V., Borel, C., Mudge, J.M., Howald, C., Foissac, S., Ucla, C., Chrast, J., Ribeca, P., Martin, D., Murray, R.R., Yang, X., Ghamsari, L., Lin, C., Bell, I., Dumais, E., Drenkow, J., Tress, M.L., Gelpí, J.L., Orozco, M., Valencia, A., van Berkum, N.L., Lajoie, B.R., Vidal, M., Stamatoyannopoulos, J., Batut, P., Dobin, A., Harrow, J., Hubbard, T., Dekker, J., Frankish, A., Salehi-Ashtiani, K., Reymond, A., Antonarakis, S.E., Guigó, R. & Gingeras, T.R. Evidence for transcript networks composed of chimeric RNAs in human cells. PloS one 7, e28213 (2012).
Dans, P.D., Pérez, A., Faustino, I., Lavery, R. & Orozco, M. Exploring polymorphisms in B-DNA helical conformations. Nucleic acids research 40, 10668-78 (2012).
Carrillo, O., Laughton, C.A. & Orozco, M. Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings. J. Chem. Theory Comput. (2012).
Sfriso, P., Emperador, A., Orellana, L., Hospital, A., Gelpí, J.L. & Orozco, M. Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 8, 4707-4718 (2012).
Pérez, A., Luque, F.J. & Orozco, M. Frontiers in Molecular Dynamics Simulations of DNA. Accounts of chemical research (2012).doi:10.1021/ar2001217
Utz, N., Meyer, T., Rink, G., Orozco, M. & Koslowski, T. Geometry, Dynamics, and Electronic Structure of DNA–Carbon Nanotube Hybrids. J. Phys. Chem. C 116 (20), pp 11278–11282, (2012).
Nadal-Ribelles, M., Conde, N., Flores, O., González-Vallinas, J., Eyras, E., Orozco, M., de Nadal, E. & Posas, F. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome biology 13, R106 (2012).

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