Publications

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2013
N. Martin-Pintado, Deleavey, G. F., Portella, G., Campos-Olivas, R., Orozco, M., Damha, M. J., and González, C., Backbone FCH⋅⋅⋅O Hydrogen Bonds in 2'F-Substituted Nucleic Acids., Angewandte Chemie (International ed. in English). 2013.
M. Rueda, Orozco, M., Totrov, M., and Abagyan, R., BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry., BMC structural biology, vol. 13. p. 32, 2013.
E. Gracia, Farré, D., Cortés, A., Ferrer-Costa, C., Orozco, M., Mallol, J., Lluís, C., Canela, E. I., McCormick, P. J., Franco, R., Fanelli, F., and 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, vol. 27, no. 3. pp. 1048-61, 2013.
B. Islam, Sgobba, M., Laughton, C., Orozco, M., Sponer, J., Neidle, S., and Haider, S., Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale., Nucleic acids research, vol. 41, no. 4. pp. 2723-35, 2013.
A. N. Naganathan and Orozco, M., The conformational landscape of an intrinsically disordered DNA-binding domain of a transcription regulator., The journal of physical chemistry. B, vol. 117, no. 44. pp. 13842-50, 2013.
M. Jamroz, Orozco, M., Kolinski, A., and Kmiecik, S., Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field. JCT, 2013.
M. Orozco, Data deluge in genomics”. Roche-Instituto Principe Felipe meeting on “Sequencing in the clinical practices”. 2013.
M. Orozco, "DNA from the electron to the chromatinVIII", Biogune Anniversary Distinguished Lecture. 2013.
M. Orozco, “DNA simulation in the postgenomic era”. Plenary lecture. Department of Pharmacy. North Caroline State University. 2013.
M. 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, vol. 10, no. 1. pp. 29-30; discussion 39-40, 2013.
A. Emperador, Solernou, A., Sfriso, P., Pons, C., Gelpí, J. L., Fernández-Recio, J., and Orozco, M., Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations, Journal of Chemical Theory and Computation, vol. 9, no. 2. pp. 1222–1229, 2013.
M. Orozco, “Expanding the frontiers of molecular dynamics simulations of DNA”. CECAM Conference. University of Vienna. 2013.
P. Sfriso, Hospital, A., Emperador, A., and Orozco, M., Exploration of conformational transition pathways from coarse-grained simulations., Bioinformatics (Oxford, England), vol. 29, no. 16. pp. 1980-6, 2013.
M. Candotti, Pérez, A., Ferrer-Costa, C., Rueda, M., Meyer, T., Gelpí, J. L., and Orozco, M., Exploring early stages of the chemical unfolding of proteins at the proteome scale., PLoS computational biology, vol. 9, no. 12. p. e1003393, 2013.
M. Orozco, “Exploring protein flexibility”. Plenary Lecture. Cambridge University. 2013.
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.
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.
M. Orozco, “In Silico Biology” Ciclo de Conferencias Montpelier. 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.
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.
M. Orozco, “The moleclar basis of the transport cycle of APC anti-porters”. Invited Talk. PRACE Scientific Conference.. 2013.
M. Orozco, “Multilevel simulation of DNA”. Invited lecture. American Chemical Society Meeting. 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.
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. Orozco, “New challenges in the representation of protein dynamics”. Plenary Lecture. Institute of Nanosciences. 2013.
T. Meyer, Gabelica, V., Grubmüller, H., and Orozco, M., Proteins in the gas phase. WIRES Comput.Mol.Sci, 2013.
A. Aviñó, Portella, G., Ferreira, R., Gargallo, R., Mazzini, S., Gabelica, V., Orozco, M., and Eritja, R., Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures., The FEBS journal. 2013.
T. Dršata, Pérez, A., Orozco, M., Morozov, A. V., Sponer, J., and Lankaš, F., Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer., Journal of chemical theory and computation, vol. 9, no. 1. pp. 707-721, 2013.
M. Candotti, Esteban-Martín, S., Salvatella, X., and 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, vol. 110, no. 15. pp. 5933-8, 2013.
G. Portella, Battistini, F., and Orozco, M., Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations., PLoS computational biology, vol. 9, no. 11. p. e1003354, 2013.
E. Durán, Djebali, S., González, S., Flores, O., Mercader, J. M., Guigó, R., Torrents, D., Soler-López, M., and Orozco, M., Unravelling the hidden DNA structural/physical code provides novel insights on promoter location., Nucleic acids research, vol. 41, no. 15. pp. 7220-30, 2013.
M. Orozco, “When mass spectroscopy and molecular simulations meet”. Invited Talk. CECAM Meeting. Frontiers of Computational Biomolecular Spectroscopy and Mass Spectrometry. 2013.
M. Orozco, “When physics and biology meet. The 2013 Nobel Award of Chemistry”. Sant Albert Plenary Lecture. Physical Engineering Sant Albert Plenary Lecture. 2013.
2012
R. Chaudhuri, Laughton, C. A., Carrillo, O., and Orozco, M., Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design, J. Chem. Theory Comput., 8 (7), pp 2204–2214 vol. 2012.
E. Gracia, Farré, D., Cortés, A., Ferrer-Costa, C., Orozco, M., Mallol, J., Lluís, C., Canela, E. I., McCormick, P. J., Franco, R., Fanelli, F., and 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.
M. Barbany, Morata, J., Meyer, T., Lois, S., Orozco, M., and 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, vol. 80, no. 9. pp. 2235-49, 2012.
R. García-Fandiño, Bernadó, P., Ayuso-Tejedor, S., Sancho, J., and Orozco, M., Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case., PLoS computational biology, vol. 8, no. 8. p. e1002647, 2012.
M. 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. 2012.
M. Kulis, 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., and Martín-Subero, J. I., Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia., Nature genetics, vol. 44, no. 11. pp. 1236-42, 2012.
S. Djebali, 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., and Gingeras, T. R., Evidence for transcript networks composed of chimeric RNAs in human cells., PloS one, vol. 7, no. 1. p. e28213, 2012.
P. D. Dans, Pérez, A., Faustino, I., Lavery, R., and Orozco, M., Exploring polymorphisms in B-DNA helical conformations., Nucleic acids research, vol. 40, no. 21. pp. 10668-78, 2012.
O. Carrillo, Laughton, C. A., and Orozco, M., Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings, J. Chem. Theory Comput. 2012.
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.
A. Pérez, Luque, F. J., and Orozco, M., Frontiers in Molecular Dynamics Simulations of DNA., Accounts of chemical research. 2012.
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.
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.

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