Publications

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Author Title [ Type(Asc)] Year
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National Conferences
M. Orozco, El papel de la supercomputación en Biomedicina. Instituto Roche-Fundación Bamberg, 2009.
Journal
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.
W. Xie, Orozco, M., Truhlar, D., and Gao, J., X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water. J. Chem. Theory Comput., 2009, 5 (3), pp 459?467, 2009.
X. S. Puente, 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., and Campo, E., Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia., Nature, vol. 475, no. 7354. pp. 101-5, 2011.
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.
M. D'Abramo, Meyer, T., Bernadó, P., Fernández-Recio, J., and Orozco, M., On the use of low resolution data to improve structure predictions of proteins and protein complexes. J. Chem. Theory Comput., 2009, 5 (11), pp 3129?3137, 2009.
C. Ferrer-Costa, Orozco, M., and de la Cruz, X., Use of bioinformatics tools for the annotation of disease-associated mutations in animal models. Proteins, 2005.
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.
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.
A. Emperador, Meyer, T., and Orozco, M., United-atom discrete molecular dynamics of proteins using physics-based potentials. J. Chem. Theory Comput., 2008, 4 (12), pp 2001?2010, 2008.
I. Faustino, Aviñó, A., Marchán, I., Luque, F. J., Eritja, R., and Orozco, M., Unique Tautomeric and Recognition Properties of Thioketothymines?. J. Am. Chem. Soc., 2009, 131 (35), pp 12845?12853, 2009.
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. J. Stollar, Gelpí, J. L., Velankar, S., Golovin, A., Orozco, M., and Luisi, B. F., Unconventional interactions between water and heterocyclic nitrogens in protein structures. Proteins, 2004.
A. Aviñó, Grimau, M., Alvira, M., Eritja, R., Gargallo, R., Orozco, M., and González, C., Triplex formation using oligonucleotide clamps carrying 8-aminopurines. Nucleoside, Nucleotides and Nucleic Acids, 26, 979-983, 2007.
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.
I. Faustino, Pérez, A., and Orozco, M., Towards a Consensus view of duplex RNA flexibility. Biophysical Journal. (2010), 99, 1876-1885., 2010.
A. Pérez, Lankas, F., Luque, F. J., and Orozco, M., Towards a consensus view of B-DNA flexibility. Nucleic Acids Res. 36(7): 2379-2394, 2008.
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.
M. Rueda, Chacón, P., and Orozco, M., Thorough Validation of Protein Normal Mode Analysis- A Comparative Study with Essential Dynamics. Structure, 15, 565-575, 2007.
M. Orozco, A theoretical view of protein dynamics., Chem Soc Rev, vol. 43, no. 14. pp. 5051-66, 2014.
A. Crespo, Martí, M., Kalko, S. G., Morreale, A., Orozco, M., Gelpí, J. L., Luque, F. J., and Estrín, D. A., Theoretical study of the truncated hemoglobin HbN: Exploring the molecular basis of the NO detoxification mechanism. J.Am.Chem.Soc., 2005.
E. Cubero, Luque, F. J., and Orozco, M., Theoretical study of the Hoogsteen<–>Watson-Crick junctions in DNA. Biophys. J., 2006.
A. Noy, Pérez, A., Laughton, C., and Orozco, M., Theoretical study of large conformational transitions in DNA: The B<->A conformational change in water and ethanol/water. Nucleic Acid Res. 35, 3330-3338, 2007.
R. García-Fandiño, Granja, J., D'Abramo, M., and Orozco, M., Theoretical Characterization of the Dynamical Behavior and Transport Properties of alpha,gamma-Peptide Nanotubes in Solution. J. Am. Chem. Soc., 2009, 131 (43), pp 15678?15686, 2009.
A. Noy, Luque, F. J., and Orozco, M., Theoretical Analysis of Antisense Duplexes: Determinants of the RNase H Susceptibility. J.Am.Chem.Soc. 130, 3486-3496., 2008.
P. Cozzini, Kellogg, G., Spyrakis, F., Abraham, D., Costantino, G., Emerson, A., Fanelli, F., Gohlke, H., Kuhn, L., Morris, G., Orozco, M., Perthinhez, T., Rizzi, M., and Sotriffer, C., Target Flexibility: An Emerging Consideration in Drug Discovery and Design. J. Med. Chem., 2008, 51 (20), pp 6237?6255, 2008.
A. Stein, Rueda, M., Panjkovich, A., Orozco, M., and Aloy, P., A systematic study of the energetics involved in structural changes upon association and connectivity in protein-protein interaction networks. In second revision, 2011.
A. Stein, Rueda, M., Panjkovich, A., Orozco, M., and Aloy, P., A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks., Structure (London, England : 1993), vol. 19, no. 6. pp. 881-9, 2011.
R. Lavery, Zakrzewska, K., Beveridge, D., Bishop, T. C., Case, D., Cheatham, T. E., Dixit, S., Jayaram, B., Lankas, F., Laughton, C., Maddocks, J. H., Michon, A., Osman, R., Orozco, M., Pérez, A., Spacková, N., and Sponer, J., A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucl. Acids Res. (2010) 38 (1): 299-313, 2009.
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.
I. Soteras, Lozano, O., Escolano, C., Orozco, M., Amat, M., Bosch, J., and Luque, F. J., Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams. J. Org. Chem., 2008, 73 (19), pp 7756?7763, 2008.
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.
A. Arcella, Portella, G., Ruiz, M. L., Eritja, R., Vilaseca, M., Gabelica, V., and Orozco, M., Structure of triplex DNA in the gas phase., Journal of the American Chemical Society, vol. 134, no. 15. pp. 6596-606, 2012.
J. Fort, de la Ballina, L. R., Burghardt, H. E., Ferrer-Costa, C., Turnay, J., Ferrer-Orta, C., Usón, I., Zorzano, A., Fernández-Recio, J., Fernández, P. L., Orozco, M., Lizarbe, M. A., Fita, I., and Palacín, M., Structure of human 4F2hc ectodomain: crystallographic and in vivo evidence for homodimerization. J.Biol.Chem, 43, 31444-31452, 2007.
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.
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.
A. Aviñó, Cubero, E., Gargallo, R., González, C., Orozco, M., and Eritja, R., Structural Properties of G.T-parallel duplexes carrying 8-aminopurine residues. J.Nucleic Acids. (2010). Article ID 7636658, 1-11., 2009.
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.
J. R. Blas, Huertas, O., Tabares, C., Sumpter, B. G., Fuentes-Cabrera, M., Orozco, M., Ordejón, P., and Luque, F. J., Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases., The journal of physical chemistry. A, vol. 115, no. 41. pp. 11344-54, 2011.
C. Pons, D'Abramo, M., Svergun, D. I., Orozco, M., Bernadó, P., and Fernández-Recio, J., Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. J.Mol.Biol (2010). 403, 217-230, 2010.
S. Ayuso-Tejedor, García-Fandiño, R., Orozco, M., Sancho, J., and Bernadó, P., Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering., Journal of molecular biology, vol. 406, no. 4. pp. 604-19, 2011.
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.
A. Bidon-Chanal, Huertas, O., Orozco, M., and Luque, F. J., Solvation enthalpies of neutral solutes in water and octanol. Theor.Chem.Acc., 123, 11-20, 2009.
E. M. Novoa, de Pouplana, L. R., and Orozco, M., Small Molecule Docking from Theoretical Structural Models, Computational Modeling of Biological Systems Biological and Medical Physics, Biomedical Engineering. pp. 75-95 , 2012.
E. Fadrná, Spacková, N., Sarzyñska, J., Koca, J., Orozco, M., Cheatham, T. E., and Sponer, J., Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields. J. Chem. Theory Comput., 2009, 5 (9), pp 2514?2530, 2009.
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., Organic Letters , vol. 17, no. 21. pp. 5416-5419, 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.
R. Pujol-Pina, Vilaprinyó-Pascual, S., Mazzucato, R., Arcella, A., Vilaseca, M., Orozco, M., and Carulla, N., SDS-PAGE analysis of Aβ oligomers is disserving research into Alzheimer´s disease: appealing for ESI-IM-MS, Scientific Reports, vol. 5. p. 14809, 2015.
C. Pons, Talavera, D., de la Cruz, X., Orozco, M., and Fernández-Recio, J., Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking., Journal of chemical information and modeling, vol. 51, no. 2. pp. 370-7, 2011.

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