Publications

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2015
J. Juárez-Jiménez, Barril, X., Orozco, M., Pouplana, R., and Luque, J. F., Assessing the suitability of the multilevel strategy for the conformational analysis of small ligands., Journal of Physical Chemistry B, vol. 119, no. 3. pp. 1164-72, 2015.
G. Portella, Terrazas, M., Villegas, N., González, C., and Orozco, M., Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH., Angew Chem Int Ed Engl, vol. 54, no. 36. pp. 10488-91, 2015.
R. Collepardo-Guevara, Portella, G., Vendruscolo, M., Frenkel, D., Schlick, T., and Orozco, M., Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study., J Am Chem Soc, vol. 137, no. 32. pp. 10205-15, 2015.
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. pp. 955-958, 2015.
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.
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, Genetics in Medicine, vol. 18. 2015.
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, vol. 526. pp. 519-524, 2015.
A. Emperador, Sfriso, P., Villarreal, M. Ariel, Gelpí, J. L., and Orozco, M., PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems, Journal of Chemical Theory and Computation , vol. 11, no. 12. pp. 5929-5938, 2015.
C. Fenollosa, Otón, M., Andrio, P., Cortés, J., Orozco, M., and J Goñi, R., SEABED: Small molEcule activity scanner weB servicE baseD, Bioinformatics, vol. 31, no. 5. pp. 773-775, 2015.
M. Habibian, Martínez-Montero, S., Portella, G., Chua, Z., D Bohle, S., Orozco, M., and Damha, M. J., Seven-Membered Ring Nucleoside Analogues: Stereoselective Synthesis and Studies on Their Conformational Properties., Org Lett, vol. 17, no. 21. pp. 5416-5419, 2015.
G. Rossetti, Dans, P. D., Gomez-Pinto, I., Ivani, I., González, C., and Orozco, M., The structural impact of DNA mismatches, Nucleic Acids Research, vol. 43, no. 8. pp. 4309-4321, 2015.
A. Arcella, Dreyer, J., Ippoliti, E., Ivani, I., Portella, G., Gabelica, V., Carloni, P., and Orozco, M., Structure and dynamics of oligonucleotides in the gas phase., Angewandte Chemie International Edition, vol. 54, no. 2. pp. 467-471, 2015.
S. Martínez-Montero, Deleavey, G. F., Dierker-Viik, A., Lindovska, P., Ilina, T., Portella, G., Orozco, M., Parniak, M. A., González, C., and Damha, M. J., Synthesis and Properties of 2'-Deoxy-2',4'-difluoroarabinose-Modified Nucleic Acids, Journal of Organic Chemistry, vol. 80, no. 6. pp. 3083-3091, 2015.
J. Gao, Orozco, M., and Peishoff, C. E., Tribute to William L. Jorgensen., Journal of Physical Chemistry B , vol. 119, no. 3. pp. 621-623, 2015.
R. Molina, Stella, S., Redondo, P., Gomez, H., Marcaida, M. José, Orozco, M., Prieto, J., and Montoya, G., Visualizing phosphodiester-bond hydrolysis by an endonuclease, Nature Structural & Molecular Biology, vol. 22, no. 1. pp. 65-72, 2015.
2014
V. Moncunill, González, S., Beà, S., Andrieux, L. O., Salaverria, I., Royo, C., Martinez, L., Puiggròs, M., Segura-Wang, M., Stütz, A. M., Navarro, A., Royo, R., Gelpí, J. L., Gut, I. G., López-Otín, C., Orozco, M., Korbel, J. O., Campo, E., Puente, X. S., and Torrents, D., Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads., Nat Biotechnol, vol. 32, no. 11. pp. 1106-12, 2014.
J. F Carmona, Davalos, V., Vidal, E., Gomez, A., Heyn, H., Hashimoto, Y., Vizoso, M., Martinez-Cardus, A., Sayols, S., Ferreira, H. J., Sánchez-Mut, J. V., Morán, S., Margelí, M., Castella, E., Berdasco, M., Stefansson, O. A., Eyfjord, J. E., Gonzalez-Suarez, E., Dopazo, J., Orozco, M., Gut, I. G., and Esteller, M., A comprehensive DNA methylation profile of epithelial-to-mesenchymal transition., Cancer Res, vol. 74, no. 19. pp. 5608-19, 2014.
B. R Fenwick, Orellana, L., Esteban-Martín, S., Orozco, M., and Salvatella, X., Correlated motions are a fundamental property of β-sheets., Nat Commun, vol. 5. p. 4070, 2014.
A. Cuervo, Dans, P. D., Carrascosa, J. L., Orozco, M., Gomila, G., and Fumagalli, L., Direct measurement of the dielectric polarization properties of DNA., Proc Natl Acad Sci U S A, vol. 111, no. 35. pp. E3624-30, 2014.
P. Sfriso, Emperador, A., Gelpí, J. Lluis, and Orozco, M., Discrete Molecular Dynamics, in Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods, CRC Press, 2014, pp. 339-356.
I. Faustino, Curutchet, C., Luque, J. F., and Orozco, M., The DNA-forming properties of 6-selenoguanine., Physical chemistry chemical physics : PCCP, vol. 16, no. 3. pp. 1101-10, 2014.
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.
A. Hospital, Gelpi, J. Ll., and Orozco, M., High Throughput Computational Studies of Macromolecular Structure Flexibility, Univeritat de Barcelona, 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.
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.
A. Arcella, Portella, G., Collepardo-Guevara, R., Chakraborty, D., Wales, D. J., and Orozco, M., Structure and properties of DNA in apolar solvents., J Phys Chem B, vol. 118, no. 29. pp. 8540-8, 2014.
M. Orozco, A theoretical view of protein dynamics., Chem Soc Rev, vol. 43, no. 14. pp. 5051-66, 2014.
P. Daniel Dans, Faustino, I., Battistini, F., Zakrzewska, K., Lavery, R., and Orozco, M., Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA., Nucleic Acids Res, vol. 42, no. 18. pp. 11304-20, 2014.
M. Pasi, Maddocks, J. H., Beveridge, D., Bishop, T. C., Case, D. A., Cheatham, T., Dans, P. D., Jayaram, B., Lankaš, F., Laughton, C., Mitchell, J., Osman, R., Orozco, M., Pérez, A., Petkevičiūtė, D., Spackova, N., Sponer, J., Zakrzewska, K., and Lavery, R., μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA., Nucleic Acids Res, vol. 42, no. 19. pp. 12272-83, 2014.
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 Comput Biol, vol. 9, no. 12. p. e1003393, 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.

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