Publications

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Grosdidier, S., Carbó, L.R., Buzón, V., Brooke, G., Nguyen, P., Baxter, J.D., Bevan, C., Webb, P., Estébanez-Perpiñá, E. & Fernández-Recio, J. Allosteric conversation in the androgen receptor ligand-binding domain surfaces. Molecular endocrinology (Baltimore, Md.) 26, 1078-90 (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 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).
Pérez-Cano, L., Eliahoo, E., Lasker, K., Wolfson, H.J., Glaser, F., Manor, H., Bernadó, P. & Fernández-Recio, J. Conformational transitions in human translin enable nucleic acid binding. Nucleic acids research 41, 9956-66 (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).
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).
Taboureau, O., Baell, J.B., Fernández-Recio, J. & Villoutreix, B.O. Established and emerging trends in computational drug discovery in the structural genomics era. Chemistry & biology 19, 29-41 (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).
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).
Small, Y.A., Guallar, V., Soudackov, A.V. & Hammes-Schiffer, S. Hydrogen bonding pathways in human dihydroorotate dehydrogenase. The journal of physical chemistry. B 110, 19704-10 (2006).
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).
Hospital, A., Andrio, P., Fenollosa, C., Cicin-Sain, D., Orozco, M. & Gelpí, J.L. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics (Oxford, England) 28, 1278-9 (2012).
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).
Pons, C., Glaser, F. & Fernández-Recio, J. Prediction of protein-binding areas by small-world residue networks and application to docking. BMC bioinformatics 12, 378 (2011).
Rao, S., Bálint, S., Cossins, B.P., Guallar, V. & Petrov, D. Raman study of mechanically induced oxygenation state transition of red blood cells using optical tweezers. Biophysical journal 96, 209-16 (2009).
Chen, Y., Tascón, I., Neunuebel, R.M., Pallara, C., Brady, J., Kinch, L.N., Fernández-Recio, J., Rojas, A.L., Machner, M.P. & Hierro, A. Structural basis for Rab1 de-AMPylation by the Legionella pneumophila effector SidD. PLoS pathogens 9, e1003382 (2013).
Castaño, T., Wang, H., Campillo, N.E., Ballester, S., González-García, C., Hernández, J., Pérez, C., Cuenca, J., Pérez-Castillo, A., Martínez, A., Huertas, O., Gelpí, J.L., Luque, F.J., Ke, H. & Gil, C. Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors. ChemMedChem 4, 866-76 (2009).
Fernández-Recio, J. & Verma, C. Theory and simulation: complexity and emergence. Current opinion in structural biology 22, 127-9 (2012).
Perez, D.I., Conde, S., Pérez, C., Gil, C., Simon, D., Wandosell, F., Moreno, F.J., Gelpí, J.L., Luque, F.J. & Martínez, A. Thienylhalomethylketones: Irreversible glycogen synthase kinase 3 inhibitors as useful pharmacological tools. Bioorganic & medicinal chemistry 17, 6914-25 (2009).
Fernández-Real, J.M., Mercader, J.M., Ortega, F.J., Moreno-Navarrete, J.M., López-Romero, P. & Ricart, W. Transferrin receptor-1 gene polymorphisms are associated with type 2 diabetes. European journal of clinical investigation 40, 600-7 (2010).
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).
Puente, X.S., Pinyol, M., Quesada, V., Conde, L., Ordóñez, G.R., Villamor, N., Escaramis, G., Jares, P., Beà, S., González-Díaz, M., Bassaganyas, L., Baumann, T., Juan, M., López-Guerra, M., Colomer, D., Tubío, J.M.C., López, C., Navarro, A., Tornador, C., Aymerich, M., Rozman, M., Hernández, J.M., Puente, D.A., Freije, J.M.P., Velasco, G., Gutiérrez-Fernández, A., Costa, D., Carrió, A., Guijarro, S., Enjuanes, A., Hernández, L., Yagüe, J., Nicolás, P., Romeo-Casabona, C.M., Himmelbauer, H., Castillo, E., Dohm, J.C., de Sanjosé, S., Piris, M.A., de Alava, E., San Miguel, J., Royo, R., Gelpí, J.L., Torrents, D., Orozco, M., Pisano, D.G., Valencia, A., Guigó, R., Bayés, M., Heath, S., Gut, M., Klatt, P., Marshall, J., Raine, K., Stebbings, L.A., Futreal, A.P., Stratton, M.R., Campbell, P.J., Gut, I., López-Guillermo, A., Estivill, X., Montserrat, E., López-Otín, C. & Campo, E. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475, 101-5 (2011).
Ballana, E., Senserrich, J., Pauls, E., Faner, R., Mercader, J.M., Uyttebroeck, F., Palou, E., Mena, M.P., Grau, E., Clotet, B., Ruiz, L., Telenti, A., Ciuffi, A. & Esté, J.A. ZNRD1 (zinc ribbon domain-containing 1) is a host cellular factor that influences HIV-1 replication and disease progression. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 50, 1022-32 (2010).