Biblio

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field, Jamroz, Michal, Orozco Modesto, Kolinski Andrzej, and Kmiecik Sebastian , Journal of Chemical Theory and Computation, 2013/01/08, Volume 9, Issue 1, p.119 - 125, (2012)

Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case., García-Fandiño, Rebeca, Bernadó Pau, Ayuso-Tejedor Sara, Sancho Javier, and Orozco Modesto , PLoS Comput Biol, 2012, Volume 8, p.e1002647, (2012)

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia., Kulis, Marta, Heath Simon, Bibikova Marina, Queirós Ana C., Navarro Alba, Clot Guillem, Martínez-Trillos Alejandra, Castellano Giancarlo, Brun-Heath Isabelle, Pinyol Magda, et al. , Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)

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)

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia., Quesada, Víctor, Conde Laura, Villamor Neus, Ordóñez Gonzalo R., Jares Pedro, Bassaganyas Laia, Ramsay Andrew J., Beà Sílvia, Pinyol Magda, Martínez-Trillos Alejandra, et al. , Nat Genet, 2012 Jan, Volume 44, p.47-52, (2012)

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia., Quesada, Víctor, Conde Laura, Villamor Neus, Ordóñez Gonzalo R., Jares Pedro, Bassaganyas Laia, Ramsay Andrew J., Beà Sílvia, Pinyol Magda, Martínez-Trillos Alejandra, et al. , Nat Genet, 2012 Jan, Volume 44, p.47-52, (2012)

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)

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations, Sfriso, Pedro, Emperador Agustí, Orellana Laura, Hospital Adam, Gelpí Josep-Lluis, and Orozco Modesto , Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012)

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations, Sfriso, Pedro, Emperador Agustí, Orellana Laura, Hospital Adam, Gelpí Josep-Lluis, and Orozco Modesto , Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012)

Frontiers in molecular dynamics simulations of DNA., Pérez, Alberto, F Luque Javier, and Orozco Modesto , Acc Chem Res, 2012 Feb 21, Volume 45, p.196-205, (2012)

Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling., Nadal-Ribelles, Mariona, Conde Núria, Flores Oscar, González-Vallinas Juan, Eyras Eduardo, Orozco Modesto, de Nadal Eulàlia, and Posas Francesc , Genome Biol, 2012, Volume 13, p.R106, (2012)

Impact of methylation on the physical properties of DNA., Pérez, Alberto, Castellazzi Chiara Lara, Battistini Federica, Collinet Kathryn, Flores Oscar, Deniz Ozgen, Ruiz Maria Luz, Torrents David, Eritja Ramon, Soler-López Montserrat, et al. , Biophys J, 2012 May 2, Volume 102, p.2140-8, (2012)

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations., Hospital, Adam, Andrio Pau, Fenollosa Carles, Cicin-Sain Damjan, Orozco Modesto, and Gelpí Josep-Lluis , Bioinformatics, 2012 May 1, Volume 28, p.1278-9, (2012)

Structure of triplex DNA in the gas phase., Arcella, Annalisa, Portella Guillem, Ruiz Maria Luz, Eritja Ramon, Vilaseca Marta, Gabelica Valérie, and Orozco Modesto , J Am Chem Soc, 2012 Apr 18, Volume 134, p.6596-606, (2012)

Backbone FC-H···O hydrogen bonds in 2’F-substituted nucleic acids., Martín-Pintado, Nerea, Deleavey Glen F., Portella Guillem, Campos-Olivas Ramón, Orozco Modesto, Damha Masad J., and González Carlos , Angew Chem Int Ed Engl, 2013 Nov 11, Volume 52, p.12065-8, (2013)

The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors., Gracia, Eduard, Farré Daniel, Cortés Antoni, Ferrer-Costa Carles, Orozco Modesto, Mallol Josefa, Lluís Carme, Canela Enric I., McCormick Peter J., Franco Rafael, et al. , FASEB J, 2013 Mar, Volume 27, p.1048-61, (2013)

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale., Islam, Barira, Sgobba Miriam, Laughton Charlie, Orozco Modesto, Sponer Jiri, Neidle Stephen, and Haider Shozeb , Nucleic Acids Res, 2013 Feb 1, Volume 41, p.2723-35, (2013)

The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator., Naganathan, Athi Narayanan, and Orozco Modesto , The Journal of Physical Chemistry B, 2013/00/15, (2013)

Dramatic effect of furanose C2’ substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom., Martín-Pintado, Nerea, Yahyaee-Anzahaee Maryam, Deleavey Glen F., Portella Guillem, Orozco Modesto, Damha Masad J., and González Carlos , J Am Chem Soc, 2013 Apr 10, Volume 135, p.5344-7, (2013)

The dynamic view of proteins: comment on "Comparing proteins to their internal dynamics: exploring structure-function relationships beyond static structural alignments"., Orozco, Modesto , Phys Life Rev, 2013 Mar, Volume 10, p.29-30; discussion 39-40, (2013)

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)

Exploration of conformational transition pathways from coarse-grained simulations., Sfriso, Pedro, Hospital Adam, Emperador Agustí, and Orozco Modesto , Bioinformatics, 2013 Aug 15, Volume 29, p.1980-6, (2013)

Exploring early stages of the chemical unfolding of proteins at the proteome scale., Candotti, Michela, Pérez Alberto, Ferrer-Costa Carles, Rueda Manuel, Meyer Tim, Gelpí Josep-Lluis, and Orozco Modesto , PLoS Computational Biology, 2013/00/01, Volume 9, p.e1003393, (2013)

Functionalization of the 3’-ends of DNA and RNA strands with N-ethyl-N-coupled nucleosides: a promising approach to avoid 3’-exonuclease-catalyzed hydrolysis of therapeutic oligonucleotides., Terrazas, Montserrat, Alagia Adele, Faustino Ignacio, Orozco Modesto, and Eritja Ramon , Chembiochem, 2013 Mar 4, Volume 14, p.510-20, (2013)

Improved nucleic acid descriptors for siRNA efficacy prediction., Sciabola, Simone, Cao Qing, Orozco Modesto, Faustino Ignacio, and Stanton Robert V. , Nucleic Acids Res, 2013 Feb 1, Volume 41, p.1383-94, (2013)

Light on the structural communication in Ras GTPases., Raimondi, Francesco, Felline Angelo, Portella Guillem, Orozco Modesto, and Fanelli Francesca , J Biomol Struct Dyn, 2013, Volume 31, p.142-57, (2013)

NAFlex: a web server for the study of nucleic acid flexibility., Hospital, Adam, Faustino Ignacio, Collepardo-Guevara Rosana, González Carlos, Gelpí Josep-Lluis, and Orozco Modesto , Nucleic Acids Res, 2013 Jul, Volume 41, p.W47-55, (2013)

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)

Proteins in the gas phase, Meyer, Tim, Gabelica Valérie, Grubmüller Helmut, and Orozco Modesto , WIREs Computational Molecular Science, Volume 3, p.408-425, (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)

Toward an atomistic description of the urea-denatured state of proteins., Candotti, Michela, Esteban-Martín Santiago, Salvatella Xavier, and Orozco Modesto , Proc Natl Acad Sci U S A, 2013 Apr 9, Volume 110, p.5933-8, (2013)

Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations, Portella, Guillem, Battistini Federica, and Orozco Modesto , PLoS Comput Biol, 11, Volume 9, p.e1003354, (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)

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads., Moncunill, Valentí, González Santi, Beà Sílvia, Andrieux Lise O., Salaverria Itziar, Royo Cristina, Martinez Laura, Puiggròs Montserrat, Segura-Wang Maia, Stütz Adrian M., et al. , Nat Biotechnol, 2014 Nov, Volume 32, p.1106-12, (2014)

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)

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)

Direct measurement of the dielectric polarization properties of DNA., Cuervo, Ana, Dans Pablo D., Carrascosa José L., Orozco Modesto, Gomila Gabriel, and Fumagalli Laura , Proc Natl Acad Sci U S A, 2014 Sep 2, Volume 111, p.E3624-30, (2014)

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)

Effects of cadmium and mercury on the upper part of skeletal muscle glycolysis in mice., Ramírez-Bajo, Maria José, de Atauri Pedro, Ortega Fernando, Westerhoff Hans V., Gelpí Josep Lluis, Centelles Josep J., and Cascante Marta , PLoS One, 2014, Volume 9, p.e80018, (2014)

Effects of cadmium and mercury on the upper part of skeletal muscle glycolysis in mice., Ramírez-Bajo, Maria José, de Atauri Pedro, Ortega Fernando, Westerhoff Hans V., Gelpí Josep Lluis, Centelles Josep J., and Cascante Marta , PLoS One, 2014, Volume 9, Issue 1, p.e80018, (2014)

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)

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., Portella, Guillem, Germann Markus W., Hud Nicholas V., and Orozco Modesto , J Am Chem Soc, 2014 Feb 26, Volume 136, p.3075-86, (2014)

Oncogenic mutations of the EGF-Receptor ectodomain reveal an unexpected mechanism for ligand-independent activation, Orellana, Laura, Hospital Adam, and Orozco Modesto , bioRxiv, 09/2014, (2014)

Oncogenic mutations of the EGF-Receptor ectodomain reveal an unexpected mechanism for ligand-independent activation, Orellana, Laura, Hospital Adam, and Orozco Modesto , bioRxiv, 09/2014, (2014)

Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures., Aviñó, Anna, Portella Guillem, Ferreira Ruben, Gargallo Raimundo, Mazzini Stefania, Gabelica Valérie, Orozco Modesto, and Eritja Ramon , FEBS J, 2014 Feb, Volume 281, p.1085-99, (2014)

Structure and properties of DNA in apolar solvents, Arcella, Annalisa, Portella Guillem, Collepardo-Guevara Rosana, Chakraborty Debayan, Wales David J., and Orozco Modesto , J Phys Chem B, 2014 Jul 24, Volume 118, p.8540-8, (2014)

A theoretical view of protein dynamics, Orozco, Modesto , Chem. Soc. Rev., Volume 43, p.5051-5066, (2014)

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)

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA., Pasi, Marco, Maddocks John H., Beveridge David, Bishop Thomas C., Case David A., Cheatham Thomas, Dans Pablo D., Jayaram B, Lankaš Filip, Laughton Charles, et al. , Nucleic Acids Res, 2014 Oct 29, Volume 42, p.12272-83, (2014)

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA., Pasi, Marco, Maddocks John H., Beveridge David, Bishop Thomas C., Case David A., Cheatham Thomas, Dans Pablo D., Jayaram B, Lankaš Filip, Laughton Charles, et al. , Nucleic Acids Res, 2014 Oct 29, Volume 42, p.12272-83, (2014)