Publications

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A
Vánzquez-Mayagoita, A. et al. 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. et al. 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>
Chaudhuri, R., Laughton, C. A., Carrillo, O. & Orozco, M. Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design. J. Chem. Theory Comput. (2012).
Orellana, L. et al. Approaching elastic network models to atomistic molecular dynamics. (2010). at <http://pubs.acs.org/doi/abs/10.1021/ct100208e>
Pérez, A. et al. 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. et al. 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>
C
Gracia, E. et al. 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
Gracia, E. et al. 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).
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. et al. 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. et al. 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. et al. 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/>
Islam, B. et al. Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. Nucleic acids research 41, 2723-35 (2013).
Naganathan, A. N. & Orozco, M. The conformational landscape of an intrinsically disordered DNA-binding domain of a transcription regulator. The journal of physical chemistry. B 117, 13842-50 (2013).
Saneyoshi, H. et al. 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. et al. A consensous view to Protein Dynamics. (2007).
Jamroz, M., Orozco, M., Kolinski, A. & Kmiecik, S. Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field. (2013).
Orozco, M., Marchán, I. & Soteras, I. (Continuum Solvation Models in Chemical Physics: Theory and Application, 2007).
Kowalcyk, L. et al. Crystal structure of a substrate-bound amino acid antiporter in the outward open conformation: mechanism of substrate recognintion and transport. (2011).
D
Orozco, M. Data deluge in genomics”. Roche-Instituto Principe Felipe meeting on “Sequencing in the clinical practices”. (2013).
Orozco, M. Datamining in cancer genome projects. Why a supercomputer center is needed. (2010). at <http://www.sc.ehu.es/ccwbayes/SymposiumBIIE/>
Noy, A. et al. 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. et al. Derivation of distributed models of atomic polarizability for molecular simulations. (2007). at <http://pubs.acs.org/doi/abs/10.1021/ct7001122>
Muñoz-Ruiz, P. et al. 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. et al. 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. et al. 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).
Orozco, M. "DNA from the electron to the chromatinVIII", Biogune Anniversary Distinguished Lecture. (2013).
Orozco, M. “DNA simulation in the postgenomic era”. Plenary lecture. Department of Pharmacy. North Caroline State University. (2013).
Faustino, I., Curutchet, C., Luque, J. F. & Orozco, M. The DNA-forming properties of 6-selenoguanine. Physical chemistry chemical physics : PCCP 16, 1101-10 (2014).
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).

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