Publications

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National Conferences
M. Orozco, El papel de la supercomputación en Biomedicina. Instituto Roche-Fundación Bamberg, 2009.
Journal
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.
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.
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.
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.
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., AMichon,, 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.
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. 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.
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.
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.
A. Pérez, Marchán, I., Svozil, D., Sponer, J., Cheatham, T. E., Laughton, C., and Orozco, M., Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophysical Journal 92, 3817-3829, 2007.
L. Conde, Vaquerizas, J. M., Ferrer-Costa, C., de la Cruz, X., Orozco, M., and Dopazo, J., PupasView: A visual tool for selecting suitable SNPs with putative pathological effects in genes for geotyping purporses. Nucleic Acid. Res., 2005.
T. Meyer, Gabelica, V., Grubmüller, H., and Orozco, M., Proteins in the gas phase. WIRES Comput.Mol.Sci, 2013.
A. N. Naganathan and Orozco, M., The protein folding transition-state ensemble from a Gō-like model., Physical chemistry chemical physics : PCCP, vol. 13, no. 33. pp. 15166-74, 2011.
A. Emperador, Meyer, T., and Orozco, M., Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials. Proteins, 78, 83-94, 2009.
D. Talavera, Hospital, A., Orozco, M., and de la Cruz, X., A Procedure for the identification of homologous alternative splicing events. BMC. Bioinformatics, 8, 260-271, 2007.
F. J. Luque, Dehez,, Chipot, C., and Orozco, M., Polarization effects in molecular interactions. Wiley Interdisciplinary Reviews: Computational Molecular Science, n/a., 2011.
C. Ferrer-Costa, Gelpí, J. L., Zamakola, L., Parrága, I., de la Cruz, X., and Orozco, M., PMUT: A Web-based tool for the annotation of pathological mutations on proteins. Bioinformatics, 2005.
O. Deniz, Flores, O., Battistini, F., Pérez, A., Soler-López, M., and Orozco, M., Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast., BMC genomics, vol. 12. p. 489, 2011.
I. Soteras, Orozco, M., and Luque, F. J., Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. J.Computer Aided Mol.Design. (2010), 24, 281-291., 2010.
I. Soteras, Forti, F., Orozco, M., and Luque, F. J., Performance of the IEF-MST Solvation Continuum Model in a Blind Test Prediction of Hydration Free Energies. J. Phys. Chem. B, 2009, 113 (27), pp 9330?9334, 2009.
P. Banás, Hollas, D., Zgarbová, M., Jurecka, P., Orozco, M., Cheatham, T. E., Sponer, J., and Otyepka, M., Performance of molecular mechanics force-fields for RNA simulations. Stability of UUCG and GNRA hairpins. J. Chem. Theory Comput., 2010, 6 (12), pp 3836?3849, 2010.
A. Klamt, Mennucci, B., Tomasi, J., Barone, V., Curutchet, C., Orozco, M., and Luque, F. J., On the performance of continuum solvation methods. A comment on Universal Approaches to Solvation Modeling. Acc. Chem. Res., 2009, 42 (4), pp 489?492, 2009.

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