Publications

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Gross, J., Aviñó, A., López de la Osa, J., González, C., Lacroix, L., Pérez, A., Orozco, M., Eritja, R. & Mergny, J.-L. 8-amino guanine accelerates quadruplex formation. (2008).at <http://dx.doi.org/10.1039/b801221k>
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Vánzquez-Mayagoita, A., Huertas, O., Brancolini, G., Sumpter, B.G., Orozco, M., Luque, F.J., Felici, Rdi & Fuentes-Cabrera, M. Ab initio study of structural, tautomeric, pairing and electronic properties of seleno-derivatives of thymine. (2009).at <http://pubs.acs.org/doi/abs/10.1021/jp9057077>
Vázquez-Mayagoitia, A., Huertas, O., Fuentes-Cabrera, M., Sumpter, B.G., Orozco, M. & Luque, F.J. Ab initio study of the structural, tautomeric, pairing, and electronic properties of seleno-derivatives of thymine. (2009).at <http://pubs.acs.org/doi/abs/10.1021/jp9057077>
Orellana, L., Rueda, M., Ferrer-Costa, C., López-Blanco, J.R., Chacón, P. & Orozco, M. Approaching elastic network models to atomistic molecular dynamics. (2010).at <http://pubs.acs.org/doi/abs/10.1021/ct100208e>
Pérez, A., Sponer, J., Jurecka, P., Hobza, P., Luque, F.J. & Orozco, M. Are the RNA(A·U) hydrogen bonds stronger than the DNA(A·T) ones?. (2005).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15977281&query_hl=2&itool=pubmed_DocSum>
Fuentes-Cabrera, M., Lipkowski, P., Huertas, O., Sumpter, B.G., Orozco, M., Luque, F.J., Wells, J.C. & Leszczynski, J. Aromaticity induced changes in the electronic properties of size-expanded DNA bases. The case of xC. (2006).
Meyer, T., de la Cruz, X. & Orozco, M. An atomistic view to the gas phase proteome. (2009).at <http://www.cell.com/structure/abstract/S0969-2126(08)00430-9>
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Huertas, O., Blas, J.R., Soteras, I., Orozco, M. & Luque, F.J. Benzoderivatives of nucleic acid bases as modified DNA building blocks. (2006).
Ortega, J.A., Blas, J.R., Orozco, M., Grandas, A., Pedroso, E. & Robles, J. Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogs are unusually sequence-dependent. (2007).at <http://www.ncbi.nlm.nih.gov/pubmed/17915883>
Orozco, M. Biomolecular simulations. An overview. (2010).at <http://bifi.es/events/biophysics2010/>
C
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 (2012).doi:10.1096/fj.12-212621
Orozco, M. Challenges in molecular dynamics of macromolecules. (2010).at <http://cwp.embo.org/pc10-24/speakers.html>
Ferrer-Costa, C., Orozco, M. & de la Cruz, X. Characterization of compensates mutations in terms of structural and physico-chemical properties. (2006).
Barbany, M., Morata, J., Meyer, T., Lois, S., Orozco, M. & 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 80, 2235-49 (2012).
Orozco, M., Orellana, L., Hospital, A., Naganathan, A.N., Emperador, A., Carrillo, O. & Gelpí, J.L. Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings. Advances in protein chemistry and structural biology 85, 183-215 (2011).
Laughton, C., Orozco, M. & Vranken, W. COCO: A simple tool to enrich the representation of conformational variability in NMR structures. (2009).at <http://www.ncbi.nlm.nih.gov/pubmed/18831040>
Velázquez-Muriel, J.A., Rueda, M., Cuesta, I., Pascual-Montano, A., Orozco, M. & Carazo, J.M. Comparison of molecular dynamics and superfamily spaces of protein domain deformation. (2009).at <http://www.biomedcentral.com/1472-6807/9/6>
Orozco, M. Computational and Medicinal Chemistry. (2009).
Orozco, M. Computational challenges in Life Sciences. (2010).at <http://www.prace-project.eu/events/documents/prace-ssc-workshop-program/>
Saneyoshi, H., Mazzini, S., Aviñó, A., Portella, G., González, C., Orozco, M., Marquez, V.E. & Eritja, R. Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer. (2009).at <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761269/?tool=pubmed>
Rueda, M., Ferrer, C., Meyer, T., Pérez, A., Camps, J., Hospital, A., Gelpí, J.L. & Orozco, M. A consensous view to Protein Dynamics. (2007).
Orozco, M., Marchán, I. & Soteras, I. Continuum analysis of conformational sampling in solution. (2007).
Kowalcyk, L., Ratera, M., Paladino, A., Bartoccioni, P., Errasti, E., Valencia, E., Portella, G., Zorzano, A., Fita, I., Orozco, M., Carpena, X., Vázquez-Ibar, J.L. & PalacÍn, M. Crystal structure of a substrate-bound amino acid antiporter in the outward open conformation: mechanism of substrate recognintion and transport. (2011).
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Orozco, M. Datamining in cancer genome projects. Why a supercomputer center is needed. (2010).at <http://www.sc.ehu.es/ccwbayes/SymposiumBIIE/>
Noy, A., Meyer, T., Rueda, M., Ferrer, C., Valencia, A., Pérez, A., de la Cruz, X., López-Bes, J.M., Luque, F.J. & Orozco, M. Datamining of molecular dynamics trajectories of nucleic acids. (2006).
Raimondi, F., Orozco, M. & Fanelli, F. Deciphering the deformation modes associated with function retention and specialization in members of the Ras Superfamily. (2010).at <http://www.cell.com/structure/abstract/S0969-2126(10)00033-X>
García-Fandiño, R., Bernadó, P., Ayuso-Tejedor, S., Sancho, J. & Orozco, M. Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case. PLoS computational biology 8, e1002647 (2012).
Soteras, I., Curutchet, C., Bidon-Chanal, A., Dehez,, Angyan, J., Orozco, M., Chipot, C. & Luque, F.J. Derivation of distributed models of atomic polarizability for molecular simulations. (2007).at <http://pubs.acs.org/doi/abs/10.1021/ct7001122>
Muñoz-Ruiz, P., 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. & Martínez, A. Design, Synthesis and Pharmacological Evaluation of Dual Binding Site Acetylcholinesterase Inhibitors: New Disease Modifying Agents for Alzheimer?s Disease. (2005).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16279781&query_hl=1&itool=pubmed_DocSum>
López de la Osa, J., González, C., Gargallo, R., Cubero, E., Aviñó, A., Orozco, M. & Eritja, R. Destabilization of quadruplex DNA by 8-aminoguanine. (2006).
Goñi, J.R., Pérez, A., Torrents, D. & Orozco, M. Determining promoter location based on DNA structure first principle calculations. (2007).
Goñi, J.R., Pérez, A., Torrents, D. & Orozco, M. Determining promoter location based on DNA structure first-principles calculations. (2007).at <http://genomebiology.com/2007/8/12/R263/>
Watts, J., Martín-Pintado, N., Gómez-Pinto, I., Schwartzentruber, J., Portella, G., Orozco, M., González, C. & Dhama, M. Differential stability of 2′F-ANA?RNA and ANA?RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. (2009).at <http://nar.oxfordjournals.org/content/38/7/2498.abstract>
Curutchet, C., Orozco, M., Luque, F.J., Mennucci, B. & Tomasi, J. Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model. (2006).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16917857&query_hl=2&itool=pubmed_DocSum>
Soliva, R., Gelpí, J.L., Almansa, C., Virgili, M. & Orozco, M. Dissection of the recognition properties of p38 MAP Kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family. (2007).at <http://www.ncbi.nlm.nih.gov/pubmed/17228870>
Orozco, M. DNA from atoms to genomics. (2009).
Orozco, M. DNA from quantum chemistry to genomics. (2008).
Goñi, J.R., Fenollosa, C., Pérez, A., Torrents, D. & Orozco, M. DNAlive: A tool for the physical analysis of DNA at the genomic scale. (2008).at <http://bioinformatics.oxfordjournals.org/content/24/15/1731.full>
Goñi, J.R., Fenollosa, C., Pérez, A., Torrents, D. & Orozco, M. DNAlive: a tool for the physical analysis of DNA at the genomic scale. (2008).
Alonso, D., Dorronsoro, I., Rubio, L., Muñoz, P., García-Palomero, E., Del Monte, M., Bidon-Chanal, A., Orozco, M., Luque, F.J., Castro, A., Medina, M. & Martínez, A. Donepezil-Tacrine hybrid related derivatives as new dual binding site inhibitors of AchE. (2005).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16230018&query_hl=2&itool=pubmed_DocSum>
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 (2012).doi:10.1016/j.plrev.2012.10.010
Orozco, M. Dynamics aspects of protein structure and interactions. (2008).
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D'Abramo, M., Orozco, M. & Amadei, A. Effects of local electric fields on the redox free energy of single stranded DNA. Chemical communications (Cambridge, England) 47, 2646-8 (2011).
Emperador, A., Solernou, A., Sfriso, P., Pons, C., Gelpí, J.L., Fernández-Recio, J. & Orozco, M. Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations. Journal of Chemical Theory and Computation 9, 1222–1229 (2013).
Orozco, M. El papel de la supercomputación en Biomedicina. (2009).
Pettifer, S. & Orozco, M. The EMBRACE web service collection. (2010).at <http://nar.oxfordjournals.org/content/38/suppl_2/W683.abstract>
Novoa, E.M., de Pouplana, L.R., Barril, X. & Orozco, M. Ensemble docking from homology models. (2010).at <http://pubs.acs.org/doi/abs/10.1021/ct100246y>
Pérez, A., Luque, F.J. & Orozco, M. Entering molecular dynamics in the biological time scale. Microsecond simulation of DNA. (2007).at <http://pubs.acs.org/doi/abs/10.1021/ja0753546>
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., Bayés, 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).
Meyer, T., Ferrer-Costa, C., Pérez, A., Rueda, M., Bidon-Chanal, A., Luque, F.J., Laughton, C. & Orozco, M. Essential Dyanmics: A Tool for Efficient Trajectory Compression and Management. (2006).

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