Publications

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Soteras, I., Lozano, O., Gomez-Esque, A., Escolano, C., Orozco, M., Amat, M., Bosch, J. & Luque, F.J. On the origin of the stereoselectivity in the alkylation of oxazolopiperidone enolates. (2006).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16704257&query_hl=2&itool=pubmed_DocSum>
Morreale, A., de la Cruz, X., Meyer, T., Gelpí, J.L., Luque, F.J. & Orozco, M. Partition of protein solvation into group contributions from molecular dynamics simulations. (2005).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15517587&query_hl=1&itool=pubmed_DocSum>
Klamt, A., Mennucci, B., Tomasi, J., Barone, V., Curutchet, C., Orozco, M. & Luque, F.J. On the performance of continuum solvation methods. A comment on Universal Approaches to Solvation Modeling. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ar800187p>
Banás, P., Hollas, D., Zgarbová, M., Jurecka, P., Orozco, M., Cheatham, T.E., Sponer, J. & Otyepka, M. Performance of molecular mechanics force-fields for RNA simulations. Stability of UUCG and GNRA hairpins. (2010).at <http://pubs.acs.org/doi/abs/10.1021/ct100481h>
Soteras, I., Forti, F., Orozco, M. & Luque, F.J. Performance of the IEF-MST Solvation Continuum Model in a Blind Test Prediction of Hydration Free Energies. (2009).at <http://pubs.acs.org/doi/abs/10.1021/jp903514u>
Soteras, I., Orozco, M. & Luque, F.J. Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. (2010).at <http://www.springerlink.com/content/t04014112597w443/>
Deniz, O., Flores, O., Battistini, F., Pérez, A., Soler-López, M. & Orozco, M. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC genomics 12, 489 (2011).
Ferrer-Costa, C., Gelpí, J.L., Zamakola, L., Parrága, I., de la Cruz, X. & Orozco, M. PMUT: A Web-based tool for the annotation of pathological mutations on proteins. (2005).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15879453&query_hl=1&itool=pubmed_DocSum>
Luque, F.J., Dehez,, Chipot, C. & Orozco, M. Polarization effects in molecular interactions. (2011).at <http://onlinelibrary.wiley.com/doi/10.1002/wcms.32/abstract>
Talavera, D., Hospital, A., Orozco, M. & de la Cruz, X. A Procedure for the identification of homologous alternative splicing events. (2007).at <http://www.biomedcentral.com/1471-2105/8/260>
Emperador, A., Meyer, T. & Orozco, M. Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials. (2009).at <http://onlinelibrary.wiley.com/doi/10.1002/prot.22563/abstract>
Naganathan, A.N. & Orozco, M. The protein folding transition-state ensemble from a Gō-like model. Physical chemistry chemical physics : PCCP 13, 15166-74 (2011).
Conde, L., Vaquerizas, J.M., Ferrer-Costa, C., de la Cruz, X., Orozco, M. & Dopazo, J. PupasView: A visual tool for selecting suitable SNPs with putative pathological effects in genes for geotyping purporses. (2005).
Pérez, A., Marchán, I., Svozil, D., Sponer, J., Cheatham, T.E., Laughton, C. & Orozco, M. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. (2007).at <http://www.ncbi.nlm.nih.gov/pubmed/17351000>
Fadrná, E., Spacková, N., Sarzyñska, J., Koca, J., Orozco, M., Cheatham, T.E. & Sponer, J. Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ct900200k>
Bidon-Chanal, A., Huertas, O., Orozco, M. & Luque, F.J. Solvation enthalpies of neutral solutes in water and octanol. (2009).at <http://www.springerlink.com/content/wx2k5l0h850x8n60/>
Ayuso-Tejedor, S., García-Fandiño, R., Orozco, M., Sancho, J. & Bernadó, P. Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering. Journal of molecular biology 406, 604-19 (2011).
Pons, C., D'Abramo, M., Svergun, D.I., Orozco, M., Bernadó, P. & Fernández-Recio, J. Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. (2010).at <http://dx.doi.org/10.1016/j.jmb.2010.08.029>
Blas, J.R., Huertas, O., Tabares, C., Sumpter, B.G., Fuentes-Cabrera, M., Orozco, M., Ordejón, P. & Luque, F.J. Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases. The journal of physical chemistry. A 115, 11344-54 (2011).
Aviñó, A., Cubero, E., Gargallo, R., González, C., Orozco, M. & Eritja, R. Structural Properties of G.T-parallel duplexes carrying 8-aminopurine residues. (2009).at <http://www.sage-hindawi.com/journals/jna/2010/763658.html>
Fort, J., 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. & Palacín, M. Structure of human 4F2hc ectodomain: crystallographic and in vivo evidence for homodimerization. (2007).at <http://www.jbc.org/content/282/43/31444.abstract>
Soteras, I., Lozano, O., Escolano, C., Orozco, M., Amat, M., Bosch, J. & Luque, F.J. Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams. (2008).at <http://pubs.acs.org/doi/abs/10.1021/jo801665k>
Lavery, R., 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. & Sponer, J. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. (2009).at <http://nar.oxfordjournals.org/content/38/1/299.abstract>
Stein, A., Rueda, M., Panjkovich, A., Orozco, M. & Aloy, P. A systematic study of the energetics involved in structural changes upon association and connectivity in protein-protein interaction networks. (2011).
Stein, A., Rueda, M., Panjkovich, A., Orozco, M. & Aloy, P. A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks. Structure (London, England : 1993) 19, 881-9 (2011).
Cozzini, P., Kellogg, G., Spyrakis, F., Abraham, D., Costantino, G., Emerson, A., Fanelli, F., Gohlke, H., Kuhn, L., Morris, G., Orozco, M., Perthinhez, T., Rizzi, M. & Sotriffer, C. Target Flexibility: An Emerging Consideration in Drug Discovery and Design. (2008).at <http://pubs.acs.org/doi/abs/10.1021/jm800562d>
Noy, A., Luque, F.J. & Orozco, M. Theoretical Analysis of Antisense Duplexes: Determinants of the RNase H Susceptibility. (2008).at <http://www.ncbi.nlm.nih.gov/pubmed/18298115>
García-Fandiño, R., Granja, J., D'Abramo, M. & Orozco, M. Theoretical Characterization of the Dynamical Behavior and Transport Properties of alpha,gamma-Peptide Nanotubes in Solution. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ja903400n>
Noy, A., Pérez, A., Laughton, C. & Orozco, M. Theoretical study of large conformational transitions in DNA: The B<->A conformational change in water and ethanol/water. (2007).at <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904281/>
Cubero, E., Luque, F.J. & Orozco, M. Theoretical study of the Hoogsteen<–>Watson-Crick junctions in DNA. (2006).
Crespo, A., Martí, M., Kalko, S.G., Morreale, A., Orozco, M., Gelpí, J.L., Luque, F.J. & Estrín, D.A. Theoretical study of the truncated hemoglobin HbN: Exploring the molecular basis of the NO detoxification mechanism. (2005).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15783226&query_hl=1&itool=pubmed_DocSum>
Rueda, M., Chacón, P. & Orozco, M. Thorough Validation of Protein Normal Mode Analysis- A Comparative Study with Essential Dynamics. (2007).at <http://www.ncbi.nlm.nih.gov/pubmed/17502102>
Pérez, A., Lankas, F., Luque, F.J. & Orozco, M. Towards a consensus view of B-DNA flexibility. (2008).at <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367714/>
Faustino, I., Pérez, A. & Orozco, M. Towards a Consensus view of duplex RNA flexibility. (2010).at <http://www.cell.com/biophysj/retrieve/pii/S0006349510008052>
Aviñó, A., Grimau, M., Alvira, M., Eritja, R., Gargallo, R., Orozco, M. & González, C. Triplex formation using oligonucleotide clamps carrying 8-aminopurines. (2007).at <http://www.ncbi.nlm.nih.gov/pubmed/18058521>
Stollar, E.J., Gelpí, J.L., Velankar, S., Golovin, A., Orozco, M. & Luisi, B.F. Unconventional interactions between water and heterocyclic nitrogens in protein structures. (2004).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15326588&query_hl=1&itool=pubmed_DocSum>
Faustino, I., Aviñó, A., Marchán, I., Luque, F.J., Eritja, R. & Orozco, M. Unique Tautomeric and Recognition Properties of Thioketothymines?. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ja904880y>
Emperador, A., Meyer, T. & Orozco, M. United-atom discrete molecular dynamics of proteins using physics-based potentials. (2008).at <http://pubs.acs.org/doi/abs/10.1021/ct8003832>
Ferrer-Costa, C., Orozco, M. & de la Cruz, X. Use of bioinformatics tools for the annotation of disease-associated mutations in animal models. (2005).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16208716&query_hl=4&itool=pubmed_docsum>
D'Abramo, M., Meyer, T., Bernadó, P., Fernández-Recio, J. & Orozco, M. On the use of low resolution data to improve structure predictions of proteins and protein complexes. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ct900305m>
Puente, X.S., 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. & Campo, E. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475, 101-5 (2011).
Xie, W., Orozco, M., Truhlar, D. & Gao, J. X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ct800239q>
National Conferences
Orozco, M. El papel de la supercomputación en Biomedicina. (2009).
Pons, C., Talavera, D., de la Cruz, X., Orozco, M. & 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 51, 370-7 (2011).

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