Publications

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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>
Puente, X. S. et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475, 101-5 (2011).
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>
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>
Durán, E. et al. Unravelling the hidden DNA structural/physical code provides novel insights on promoter location. Nucleic acids research 41, 7220-30 (2013).
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>
Faustino, I. et al. Unique Tautomeric and Recognition Properties of Thioketothymines?. (2009). at <http://pubs.acs.org/doi/abs/10.1021/ja904880y>
Portella, G., Battistini, F. & Orozco, M. Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations. PLoS computational biology 9, e1003354 (2013).
Stollar, E. J. et al. 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>
Aviñó, A. et al. Triplex formation using oligonucleotide clamps carrying 8-aminopurines. (2007). at <http://www.ncbi.nlm.nih.gov/pubmed/18058521>
Faustino, I., Pérez, A. & Orozco, M. Towards a Consensus view of duplex RNA flexibility. (2010). at <http://www.cell.com/biophysj/retrieve/pii/S0006349510008052>
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/>
Candotti, M., Esteban-Martín, S., Salvatella, X. & 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 110, 5933-8 (2013).
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>
Crespo, A. et al. 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>
Cubero, E., Luque, F. J. & Orozco, M. Theoretical study of the Hoogsteen<–>Watson-Crick junctions in DNA. (2006).
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/>
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., 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>
Cozzini, P. et al. Target Flexibility: An Emerging Consideration in Drug Discovery and Design. (2008). at <http://pubs.acs.org/doi/abs/10.1021/jm800562d>
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).
Lavery, R. et al. 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>
Soteras, I. et al. Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams. (2008). at <http://pubs.acs.org/doi/abs/10.1021/jo801665k>
Dršata, T. et al. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. Journal of chemical theory and computation 9, 707-721 (2013).
Arcella, A. et al. Structure of triplex DNA in the gas phase. Journal of the American Chemical Society 134, 6596-606 (2012).
Fort, J. et al. Structure of human 4F2hc ectodomain: crystallographic and in vivo evidence for homodimerization. (2007). at <http://www.jbc.org/content/282/43/31444.abstract>
Aviñó, A. et al. Structural Properties of G.T-parallel duplexes carrying 8-aminopurine residues. (2009). at <http://www.sage-hindawi.com/journals/jna/2010/763658.html>
Blas, J. R. et al. Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases. The journal of physical chemistry. A 115, 11344-54 (2011).
Pons, C. et al. 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>
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).
Aviñó, A. et al. Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures. The FEBS journal (2013). doi:10.1111/febs.12670
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/>
Novoa, E. M., de Pouplana, L. R. & Orozco, M. Small Molecule Docking from Theoretical Structural Models. Computational Modeling of Biological Systems Biological and Medical Physics, Biomedical Engineering 75-95 (2012).
Fadrná, E. et al. 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>
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).
Pérez, A. et al. 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>
Conde, L. et al. PupasView: A visual tool for selecting suitable SNPs with putative pathological effects in genes for geotyping purporses. (2005).
Meyer, T., Gabelica, V., Grubmüller, H. & Orozco, M. Proteins in the gas phase. (2013).
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).
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>
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>
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>
Ferrer-Costa, C. et al. 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>
Deniz, O. et al. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC genomics 12, 489 (2011).
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/>
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>
Banás, P. et al. 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>
Klamt, A. et al. 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>

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