Publications

Export 185 results:
Author Title [ Type(Desc)] Year
Filters: Author is Modesto Orozco  [Clear All Filters]
Journal
Carrillo, O. & Orozco, M. GRID-based molecular dynamics. A Tool for genomic-scale simulations of channels in proteins. (2008). at <http://www.ncbi.nlm.nih.gov/pubmed/17803238>
Nadal-Ribelles, M. et al. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome biology 13, R106 (2012).
Nadal-Ribelles, M. et al. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome biology 13, R106 (2012).
Muñoz-Muriedas, J., Barril, X., López, J. M., Orozco, M. & Luque, F. J. A hydrophobic similarity analysis of solvation effects on nucleic acids. (2006).
Pérez, A. et al. Impact of methylation on the physical properties of DNA. Biophysical journal 102, 2140-8 (2012).
Noy, A., Soteras, I., Luque, F. J. & Orozco, M. The impact of monovalent ion force-field model in nucleic acids simulations. (2009). at <http://pubs.rsc.org/en/Content/ArticleLanding/2009/CP/b912067j>
Sciabola, S., Cao, Q., Orozco, M., Faustino, I. & Stanton, R. V. Improved nucleic acid descriptors for siRNA efficacy prediction. Nucleic acids research 41, 1383-94 (2013).
Talavera, D., Vogel, C., Orozco, M., Teichmann, S. A. & de la Cruz, X. The (In)dependence of alternative splicing and gene duplication. (2007). at <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0030033>
Soteras, I., Chipot, C., Orozco, M. & Luque, F. J. Induction effects in metal cation-benzene complexes. (2008). at <http://dx.doi.org/10.1039/b719461g>
Bidon-Chanal, A. et al. Ligand-induced dynamical regulation of NO conversion in Mycobacterium Tubercolisis truncated-hemoglobin-N. (2006). at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16688782&query_hl=1&itool=pubmed_docsum>
Raimondi, F., Felline, A., Portella, G., Orozco, M. & Fanelli, F. Light on the structural communication in Ras GTPases. Journal of biomolecular structure & dynamics 31, 142-57 (2013).
Raimondi, F., Felline, A., Portella, G., Orozco, M. & Fanelli, F. Light on the structural communication in Ras GTPases. Journal of biomolecular structure & dynamics 31, 142-57 (2013).
Morreale, A. et al. Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?. (2004). at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15382247&query_hl=1&itool=pubmed_DocSum>
Huertas, O. et al. Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives. (2006).
Portella, G., Germann, M. W., Hud, N. V. & Orozco, M. MD and NMR Analyses of Choline and TMA Binding to Duplex DNA: On the Origins of Aberrant Sequence-Dependent Stability by Alkyl Cations in Aqueous and Water-Free Solvents. Journal of the American Chemical Society (2014). doi:10.1021/ja410698u
Portella, G., Germann, M. W., Hud, N. V. & Orozco, M. MD and NMR Analyses of Choline and TMA Binding to Duplex DNA: On the Origins of Aberrant Sequence-Dependent Stability by Alkyl Cations in Aqueous and Water-Free Solvents. Journal of the American Chemical Society (2014). doi:10.1021/ja410698u
Hospital, A. et al. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics (Oxford, England) 28, 1278-9 (2012).
Meyer, T. et al. MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. Structure (London, England : 1993) 18, 1399-409 (2010).
Meyer, T. et al. MoDEL (Molecular Dynamics Extended Library). A database of atomistic molecular dynamics simulations. (2010). at <http://www.cell.com/structure/abstract/S0969-2126(10)00353-9>
Muñoz-Muriedas, J. et al. Molecular Alignment Based on Hydrophobic Similarity as a Tool in Drug Design. (2005).
Kowalczyk, L. et al. Molecular basis of substrate-induced permeation by an amino acid antiporter. Proceedings of the National Academy of Sciences of the United States of America 108, 3935-40 (2011).
Curutchet, C., Bidon-Chanal, A., Soteras, I., Orozco, M. & Luque, F. J. MST continuum study of the hydration free energies of monovalent ionic species. (2005). at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16851394&query_hl=1&itool=pubmed_DocSum>
Forti, F., Cavasotto, C. N., Orozco, M., Barril, X. & Luque, J. F. A Multilevel Strategy for the Exploration of the Conformational Flexibility of Small Molecules. J. Chem. Theory Comput (2012).
Portella, G. & Orozco, M. Multiple routes characterize the folding of a small DNA hairpin. (2010). at <http://onlinelibrary.wiley.com/doi/10.1002/anie.201003816/abstract>
Hospital, A. et al. NAFlex: a web server for the study of nucleic acid flexibility. Nucleic acids research 41, W47-55 (2013).
Naganathan, A. N. & Orozco, M. The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding. Journal of the American Chemical Society 133, 12154-61 (2011).
Sponer, J. et al. Nature of base stacking. Reference quantum chemical stacking energies in ten unique B-DNA base pair steps. (2006).
D'Abramo, M., Castellazzi, C. L., Orozco, M. & Amadei, A. On the nature of DNA hyperchromic effect. The journal of physical chemistry. B 117, 8697-704 (2013).
Rueda, M., Luque, F. J. & Orozco, M. The nature of minor-groove binders-DNA complexes in the gas phase. (2005). at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16104746&query_hl=2&itool=pubmed_docsum>
Laughton, C. & Orozco, M. Nucleic Acid Themed Issue. Editorial. (2009). at <http://pubs.rsc.org/en/Content/ArticleLanding/2009/CP/b921472k>
Raimondi, F., Portella, G., Orozco, M. & Fanelli, F. Nucleotide binding switches the information flow in ras GTPases. PLoS computational biology 7, e1001098 (2011).
Raimondi, F., Portella, G., Orozco, M. & Fanelli, F. Nucleotide switches the information flow in Ras GTPases. (2011).
Flores, O. & Orozco, M. nucleR: a package for non-parametric nucleosome positioning. Bioinformatics (Oxford, England) 27, 2149-50 (2011).
Soteras, I. et al. 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. et al. 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. 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>
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>
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. 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).
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>
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).
Meyer, T., Gabelica, V., Grubmüller, H. & Orozco, M. Proteins in the gas phase. (2013).
Conde, L. et al. PupasView: A visual tool for selecting suitable SNPs with putative pathological effects in genes for geotyping purporses. (2005).
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>
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).
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>

Pages