Found 301 results
[ Author(Asc)] Title Year
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nucleR: a package for non-parametric nucleosome positioning., Flores, Oscar, and Orozco Modesto , Bioinformatics, 2011 Aug 1, Volume 27, p.2149-50, (2011)
Fuzziness and noise in nucleosomal architecture., Flores, Oscar, Deniz Ozgen, Soler-López Montserrat, and Orozco Modesto , Nucleic Acids Res, 2014 Apr, Volume 42, p.4934-46, (2014)
DASiR: Distributed Annotation System in R, Flores, Oscar, and Mantsoki Anna , (2013)
Characterization of compensated mutations in terms of structural and physico-chemical properties., Ferrer-Costa, Carles, Orozco Modesto, and de la Cruz Xavier , J Mol Biol, 2007 Jan 5, Volume 365, p.249-56, (2007)
Use of bioinformatics tools for the annotation of disease-associated mutations in animal models., Ferrer-Costa, Carles, Orozco Modesto, and de la Cruz Xavier , Proteins, 2005 Dec 1, Volume 61, p.878-87, (2005)
PMUT: a web-based tool for the annotation of pathological mutations on proteins., Ferrer-Costa, Carles, Gelpí Josep-Lluis, Zamakola Leire, Párraga Iván, de la Cruz Xavier, and Orozco Modesto , Bioinformatics, 2005 Jul 15, Volume 21, p.3176-8, (2005)
Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties., Ferrer-Costa, Carles, Orozco Modesto, and de la Cruz Xavier , J Mol Biol, 2002 Jan 25, Volume 315, p.771-86, (2002)
Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor, Fernández-Zapata, Jesús, Pérez-Castaño Ricardo, Aranda Juan, Colizzi Francesco, Polanco María Carmen, Orozco Modesto, Padmanabhan S., and Elías-Arnanz Montserrat , Journal of Biological Chemistry, 11/2018, Volume 293, Issue 46, p.17888 - 17905, (2018)
Correlated motions are a fundamental property of B-sheets, R. Fenwick, Bryn, Orellana Laura, Esteban-Martí-n Santi, Orozco Modesto, and Salvatella Xavier , Nat Commun, 10/2014, Volume 5, (2014)
SEABED: Small molEcule activity scanner weB servicE baseD., Fenollosa, Carlos, Otón Marcel, Andrio Pau, Cortés Jorge, Orozco Modesto, and J Goñi Ramon , Bioinformatics, 2015 Mar 1, Volume 31, p.773-5, (2015)
The DNA-forming properties of 6-selenoguanine, Faustino, Ignacio, Curutchet Carles, F Luque Javier, and Orozco Modesto , Phys. Chem. Chem. Phys., Volume 16, p.1101-1110, (2014)
Unique tautomeric and recognition properties of thioketothymines?, Faustino, Ignacio, Aviñó Anna, Marchán Ivan, F Luque Javier, Eritja Ramon, and Orozco Modesto , J Am Chem Soc, 2009 Sep 9, Volume 131, p.12845-53, (2009)
Toward a consensus view of duplex RNA flexibility., Faustino, Ignacio, Pérez Alberto, and Orozco Modesto , Biophys J, 2010 Sep 22, Volume 99, p.1876-85, (2010)
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields, Fadrná, Eva, Špačková Nad’a, Sarzyñska Joanna, Koča Jaroslav, Orozco Modesto, Cheatham Thomas E., Kulinski Tadeusz, and Šponer Jiří , Journal of Chemical Theory and Computation, 2009/09/08, Volume 5, Issue 9, p.2514 - 2530, (2009)
Functional and structural conservation of CBS domains from CLC chloride channels., Estévez, Raúl, Pusch Michael, Ferrer-Costa Carles, Orozco Modesto, and Jentsch Thomas J. , J Physiol, 2004 Jun 1, Volume 557, p.363-78, (2004)
Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor, Escobedo, Albert, Topal Busra, Kunze Micha B. A., Aranda Juan, Chiesa Giulio, Mungianu Daniele, Bernardo-Seisdedos Ganeko, Eftekharzadeh Bahareh, Gairí Margarida, Pierattelli Roberta, et al. , Nature Communication, 05/2019, Volume 10, Issue 1, p.2034, (2019)
Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad., Escaja, Núria, Gelpí Josep-Lluis, Orozco Modesto, Rico Manuel, Pedroso Enrique, and González Carlos , J Am Chem Soc, 2003 May 14, Volume 125, p.5654-62, (2003)
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics., Emperador, Agustí, Carrillo Oliver, Rueda Manuel, and Orozco Modesto , Biophys J, 2008 Sep, Volume 95, p.2127-38, (2008)
Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins, Emperador, Agustí, and Orozco Modesto , Journal of Chemical Theory and Computation, 03/2017, Volume 13, Issue 3, p.1454 - 1461, (2017)
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials., Emperador, Agustí, Meyer Tim, and Orozco Modesto , Proteins, 2010 Jan, Volume 78, p.83-94, (2010)
Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations, Emperador, Agustí, Solernou Albert, Sfriso Pedro, Gelpí Josep-Lluis, Fernandez-Recio J, and Orozco Modesto , Journal of Chemical Theory and Computation, Volume 9, p.1222-1229, (2013)
PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems., Emperador, Agustí, Sfriso Pedro, Villarreal Marcos Ariel, Gelpí Josep-Lluis, and Orozco Modesto , J Chem Theory Comput, 2015 Dec 8, Volume 11, p.5929-38, (2015)
On the Use of low-resolution Data to Improve Structure Prediction of Proteins and Protein Complexes, D’Abramo, Marco, Meyer Tim, Bernadó Pau, Pons Carles, Recio Juan Fernánde, and Orozco Modesto , Journal of Chemical Theory and Computation, 2009/11/10, Volume 5, Issue 11, p.3129 - 3137, (2009)
Effects of local electric fields on the redox free energy of single stranded DNA., D’Abramo, Marco, Orozco Modesto, and Amadei Andrea , Chem Commun (Camb), 2011 Mar 7, Volume 47, p.2646-8, (2011)
On the nature of DNA hyperchromic effect., D’Abramo, Marco, Castellazzi Chiara Lara, Orozco Modesto, and Amadei Andrea , J Phys Chem B, 2013 Jul 25, Volume 117, p.8697-704, (2013)
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location., Durán, Elisa, Djebali Sarah, González Santi, Flores Oscar, Mercader Josep Maria, Guigó Roderic, Torrents David, Soler-López Montserrat, and Orozco Modesto , Nucleic Acids Res, 2013 Aug, Volume 41, p.7220-30, (2013)
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer., Dršata, Tomáš, Pérez Alberto, Orozco Modesto, Morozov Alexandre V., Sponer Jiřĺ, and Lankaš Filip , J Chem Theory Comput, 2013, Volume 9, p.707-721, (2013)
Evidence for transcript networks composed of chimeric RNAs in human cells., Djebali, Sarah, Lagarde Julien, Kapranov Philipp, Lacroix Vincent, Borel Christelle, Mudge Jonathan M., Howald Cédric, Foissac Sylvain, Ucla Catherine, Chrast Jacqueline, et al. , PLoS One, 2012, Volume 7, p.e28213, (2012)
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast., Deniz, Ozgen, Flores Oscar, Battistini Federica, Pérez Alberto, Soler-López Montserrat, and Orozco Modesto , BMC Genomics, 2011, Volume 12, p.489, (2011)
Nucleosome architecture throughout the cell cycle, Deniz, Ozgen, Flores Oscar, Aldea Martí, Soler-López Montserrat, and Orozco Modesto , Scientific Reports, 01/2016, Volume 6, p.19729 -, (2016)
Subcellular localization of the interaction between the human immunodeficiency virus transactivator Tat and the nucleosome assembly protein 1, De Marco, Alex, Dans Pablo Daniel, Knezevich Anna, Maiuri Paolo, Pantano Sergio, and Marcello Alessandro , Amino acids, Volume 38, Number 5, p.1583–1593, (2010)
Destabilization of quadruplex DNA by 8-aminoguanine., de la Osa, Jaime Lopez, González Carlos, Gargallo Raimundo, Rueda Manuel, Cubero Elena, Orozco Modesto, Aviñó Anna, and Eritja Ramon , Chembiochem, 2006 Jan, Volume 7, p.46-8, (2006)
Time averaging of NMR chemical shifts in the MLF peptide in the solid state., De Gortari, Itzam, Portella Guillem, Salvatella Xavier, Bajaj Vikram S., van der Wel Patrick C. A., Yates Jonathan R., Segall Matthew D., Pickard Chris J., Payne Mike C., and Vendruscolo Michele , J Am Chem Soc, 2010 May 5, Volume 132, p.5993-6000, (2010)
Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?, Darré, Leonardo, Machado Matias R., Dans Pablo Daniel, Herrera Fernando E., and Pantano Sergio , Journal of Chemical Theory and Computation, Volume 6, Number 12, p.3793–3807, (2010)
Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA, Darré, Leonardo, Ivani Ivan, Dans Pablo D., Gómez Hansel, Hospital Adam, and Orozco Modesto , Journal of the American Chemical Society, 12/2016, Volume 138, Issue 50, p.16355 - 16363, (2016)
Multiscale simulation of DNA, Dans, Pablo D., Walther Jurgen, Gómez Hansel, and Orozco Modesto , Current Opinions in Structural Biology - Theory and simulation • Macromolecular machines 2016, 02/2016, Volume 37, p.29 - 45, (2016)
Density functional theory characterization and descriptive analysis of cisplatin and related compounds, Dans, Pablo Daniel, and E Coitiño Laura , Journal of chemical information and modeling, Volume 49, Number 6, p.1407–1419, (2009)
Long-timescale dynamics of the Drew-Dickerson dodecamer., Dans, Pablo D., Danilāne Linda, Ivani Ivan, Dršata Tomáš, Lankaš Filip, Hospital Adam, Walther Jurgen, Pujagut Ricard Illa, Battistini Federica, Gelpí Josep-Lluis, et al. , Nucleic Acids Res, 2016 May 19, Volume 44, p.4052-66, (2016)
Assessing the Accuracy of the SIRAH Force Field to Model DNA at Coarse Grain Level, Dans, Pablo Daniel, Darré Leonardo, Machado Matias R., Zeida Ari, Brandner Astrid F., and Pantano Sergio , Advances in Bioinformatics and Computational Biology, p.71–81, (2013)
A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics, Dans, Pablo Daniel, Zeida Ari, Machado Matías R., and Pantano Sergio , Journal of Chemical Theory and Computation, Volume 6, Number 5, p.1711–1725, (2010)
Exploring polymorphisms in B-DNA helical conformations., Dans, Pablo D., Pérez Alberto, Faustino Ignacio, Lavery Richard, and Orozco Modesto , Nucleic Acids Res, 2012 Nov, Volume 40, p.10668-78, (2012)
Structural and Energetic Study of Cisplatin and Derivatives: Comparison of the Performance of Density Funtional Theory Implementations, Dans, Pablo Daniel, Crespo Alejandro, Estrin Darío A., and E Coitiño Laura , Journal of Chemical Theory and Computation, Volume 4, Number 5, p.740–750, (2008)
Modeling, Simulations, and Bioinformatics at the Service of RNA Structure, Dans, Pablo D., Gallego Diego, Balaceanu Alexandra, Darré Leonardo, Gómez Hansel, and Orozco Modesto , Chem , 10/2018, (2018)
How accurate are accurate force-fields for B-DNA?, Dans, Pablo D., Ivani Ivan, Hospital Adam, Portella Guillem, González Carlos, and Orozco Modesto , Nucleic Acids Research, 01/2017, Volume 45, Issue 7, p.4217-4230, (2017)
Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA, Dans, Pablo D., Faustino Ignacio, Battistini Federica, Zakrzewska Krystyna, Lavery Richard, and Orozco Modesto , Nucleic Acid Research, 09/2014, (2014)