Publications

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A
A. Vánzquez-Mayagoita, Huertas, O., Brancolini, G., Sumpter, B. G., Orozco, M., Luque, F. J., Felici, Rdi, and Fuentes-Cabrera, M., Ab initio study of structural, tautomeric, pairing and electronic properties of seleno-derivatives of thymine. J. Phys. Chem. B, 2009, 113 (43), pp 14465?14472, 2009.
A. Vázquez-Mayagoitia, Huertas, O., Fuentes-Cabrera, M., Sumpter, B. G., Orozco, M., and Luque, F. J., Ab initio study of the structural, tautomeric, pairing, and electronic properties of seleno-derivatives of thymine. J.Phys.Chem.B, 112, 2179-2186, 2009.
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.
L. Orellana, Rueda, M., Ferrer-Costa, C., López-Blanco, J. R., Chacón, P., and Orozco, M., Approaching elastic network models to atomistic molecular dynamics. J. Chem. Theory Comput., 2010, 6 (9), pp 2910?2923, 2010.
A. Pérez, Sponer, J., Jurecka, P., Hobza, P., Luque, F. J., and Orozco, M., Are the RNA(A·U) hydrogen bonds stronger than the DNA(A·T) ones?. Chemistry an European Journal, 2005.
M. Fuentes-Cabrera, Lipkowski, P., Huertas, O., Sumpter, B. G., Orozco, M., Luque, F. J., Wells, J. C., and Leszczynski, J., Aromaticity induced changes in the electronic properties of size-expanded DNA bases. The case of xC. International Journal of Quantum Chemistry, 2006.
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.
T. Meyer, de la Cruz, X., and Orozco, M., An atomistic view to the gas phase proteome. Structure, 17, 88-95, 2009.
B
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.
O. Huertas, Blas, J. R., Soteras, I., Orozco, M., and Luque, F. J., Benzoderivatives of nucleic acid bases as modified DNA building blocks. J.Phys.Chem.A, 2006.
A. Hospital, Andrio, P., Cugnasco, C., Codo, L., Becerra, Y., Dans, P., Battistini, F., Torres, J., Goñi, R., Orozco, M., and Gelpí, J. Lluis, BIGNASim: A NoSQL database structure and analysis portal for nucleic acids simulation data Hospital, Nucleic Acids Research, vol. 44, no. 1. pp. D272-D278, 2016.
J. A. Ortega, Blas, J. R., Orozco, M., Grandas, A., Pedroso, E., and Robles, J., Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogs are unusually sequence-dependent. Organic Letters, 9, 4503-4506, 2007.
M. Orozco, Biomolecular simulations. An overview. IV Spanish Portuguese Biophysical Congress, 2010.
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.
C
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.
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.
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.
M. Orozco, Challenges in molecular dynamics of macromolecules. EMBO Course on Molecular Modeling, 2010.
C. Ferrer-Costa, Orozco, M., and de la Cruz, X., Characterization of compensates mutations in terms of structural and physico-chemical properties. J.Mol.Biol, 2006.
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. 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. Orozco, Orellana, L., Hospital, A., Naganathan, A. N., Emperador, A., Carrillo, O., and Gelpí, J. L., Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings., Advances in protein chemistry and structural biology, vol. 85. pp. 183-215, 2011.
C. Laughton, Orozco, M., and Vranken, W., COCO: A simple tool to enrich the representation of conformational variability in NMR structures. Proteins, 75, 206-216, 2009.
J. A. Velázquez-Muriel, Rueda, M., Cuesta, I., Pascual-Montano, A., Orozco, M., and Carazo, J. M., Comparison of molecular dynamics and superfamily spaces of protein domain deformation. BMC Struct. Biol., (2009), 9, 6-20., 2009.
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.
M. Orozco, Computational and Medicinal Chemistry. American Chemical Society Meeting, 2009.
M. Orozco, Computational challenges in Life Sciences. HPC-Prace meeting, 2010.
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.
H. Saneyoshi, Mazzini, S., Aviñó, A., Portella, G., González, C., Orozco, M., Marquez, V. E., and Eritja, R., Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer. Nucleic Acids Res. 2009 September; 37(17): 5589?5601, 2009.
M. Rueda, Ferrer, C., Meyer, T., Pérez, A., Camps, J., Hospital, A., Gelpí, J. L., and Orozco, M., A consensous view to Protein Dynamics. Proc. Natl. Acad. Sci. USA, 2007.
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, Marchán, I., and Soteras, I., Continuum analysis of conformational sampling in solution, Continuum Solvation Models in Chemical Physics: Theory and Application, 2007.
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.
L. Kowalcyk, Ratera, M., Paladino, A., Bartoccioni, P., Errasti, E., Valencia, E., Portella, G., Zorzano, A., Fita, I., Orozco, M., Carpena, X., Vázquez-Ibar, J. L., and PalacÍn, M., Crystal structure of a substrate-bound amino acid antiporter in the outward open conformation: mechanism of substrate recognintion and transport. In Press., 2011.
D
M. Orozco, Data deluge in genomics”. Roche-Instituto Principe Felipe meeting on “Sequencing in the clinical practices”. 2013.
M. Orozco, Datamining in cancer genome projects. Why a supercomputer center is needed. III International Symposium on Biomedical Informatics in Europe, 2010.
A. Noy, Meyer, T., Rueda, M., Ferrer, C., Valencia, A., Pérez, A., de la Cruz, X., López-Bes, J. M., Luque, F. J., and Orozco, M., Datamining of molecular dynamics trajectories of nucleic acids. J.Biomol.Struct.Dynam, 2006.
F. Raimondi, Orozco, M., and Fanelli, F., Deciphering the deformation modes associated with function retention and specialization in members of the Ras Superfamily. Structure. (2010), 18, 402-414, 2010.
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.
I. Soteras, Curutchet, C., Bidon-Chanal, A., Dehez, F., Angyan, J., Orozco, M., Chipot, C., and Luque, F. J., Derivation of distributed models of atomic polarizability for molecular simulations. J.Chem.Theor.Comp, 3, 1901-1913, 2007.
P. Muñoz-Ruiz, Rubio, L., García-Palomero, E., del Monte-Millán, M., Usán, P., Dorronsoro, I., Bartolini, M., Bidon-Chanal, A., Orozco, M., Luque, F. J., Medina, M., and Martínez, A., Design, Synthesis and Pharmacological Evaluation of Dual Binding Site Acetylcholinesterase Inhibitors: New Disease Modifying Agents for Alzheimer?s Disease. J.Med.Chem, 2005.
J. López de la Osa, González, C., Gargallo, R., Cubero, E., Aviñó, A., Orozco, M., and Eritja, R., Destabilization of quadruplex DNA by 8-aminoguanine. ChemBiochem, 2006.
J. R. Goñi, Pérez, A., Torrents, D., and Orozco, M., Determining promoter location based on DNA structure first principle calculations. Genome Biology, 8:R263, 2007.
J. R. Goñi, Pérez, A., Torrents, D., and Orozco, M., Determining promoter location based on DNA structure first-principles calculations. Genome Biology 8, R263, 2007.
J. Watts, Martín-Pintado, N., Gómez-Pinto, I., Schwartzentruber, J., Portella, G., Orozco, M., González, C., and Dhama, M., Differential stability of 2′F-ANA?RNA and ANA?RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. Nucl. Acids Res. (2010) 38 (7): 2498-2511, 2009.
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.

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