Biblio

Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer., Saneyoshi, Hisao, Mazzini Stefania, Aviñó Anna, Portella Guillem, González Carlos, Orozco Modesto, Marquez Victor E., and Eritja Ramon , Nucleic Acids Res, 2009 Sep, Volume 37, p.5589-601, (2009)

On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling"., Klamt, Andreas, Mennucci Benedetta, Tomasi Jacopo, Barone Vincenzo, Curutchet Carles, Orozco Modesto, and F Luque Javier , Acc Chem Res, 2009 Apr 21, Volume 42, p.489-92; discussion 493-7, (2009)

Role of Pre-A motif in nitric oxide scavenging by truncated hemoglobin, HbN, of Mycobacterium tuberculosis., Lama, Amrita, Pawaria Sudesh, Bidon-Chanal Axel, Anand Arvind, Gelpí Josep-Lluis, Arya Swati, Martí Marcelo, Estrin Darío A., F Luque Javier, and Dikshit Kanak L. , J Biol Chem, 2009 May 22, Volume 284, p.14457-68, (2009)

Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors., Castaño, Tania, Wang Huanchen, Campillo Nuria E., Ballester Sara, González-García Coral, Hernández Javier, Pérez Concepción, Cuenca Jimena, Pérez-Castillo Ana, Martínez Ana, et al. , ChemMedChem, 2009 May, Volume 4, p.866-76, (2009)

Thienylhalomethylketones: Irreversible glycogen synthase kinase 3 inhibitors as useful pharmacological tools., Perez, Daniel I., Conde Santiago, Pérez Concepción, Gil Carmen, Simon Diana, Wandosell Francisco, Moreno Francisco J., Gelpí Josep-Lluis, Luque Francisco J., and Martínez Ana , Bioorg Med Chem, 2009 Oct 1, Volume 17, p.6914-25, (2009)

Thienylhalomethylketones: Irreversible glycogen synthase kinase 3 inhibitors as useful pharmacological tools., Perez, Daniel I., Conde Santiago, Pérez Concepción, Gil Carmen, Simon Diana, Wandosell Francisco, Moreno Francisco J., Gelpí Josep-Lluis, Luque Francisco J., and Martínez Ana , Bioorg Med Chem, 2009 Oct 1, Volume 17, p.6914-25, (2009)

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)

The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamer., Saneyoshi, Hisao, Mazzini Stefania, Aviñó Anna, Portella Guillem, González Carlos, Orozco Modesto, Marquez Victor E., and Eritja Ramon , Nucleic Acids Symp Ser (Oxf), 2009, p.109-10, (2009)

The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamer., Saneyoshi, Hisao, Mazzini Stefania, Aviñó Anna, Portella Guillem, González Carlos, Orozco Modesto, Marquez Victor E., and Eritja Ramon , Nucleic Acids Symp Ser (Oxf), 2009, p.109-10, (2009)

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)

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)

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)

Differential stability of 2’F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility., Watts, Jonathan K., Martín-Pintado Nerea, Gómez-Pinto Irene, Schwartzentruber Jeremy, Portella Guillem, Orozco Modesto, González Carlos, and Damha Masad J. , Nucleic Acids Res, 2010 Apr, Volume 38, p.2498-511, (2010)

The EMBRACE web service collection, Pettifer, Steve, Ison Jon, Kalaš Matúš, Thorne Dave, McDermott Philip, Jonassen Inge, Liaquat Ali, Fernández José M., Rodriguez Jose M., Partners INB-, et al. , Nucleic Acids Research, Volume 38, p.W683-W688, (2010)

Isoform-specific determinants in the HP1 binding to histone 3: insights from molecular simulations, Machado, Matias R., Dans Pablo Daniel, and Pantano Sergio , Amino acids, Volume 38, Number 5, p.1571–1581, (2010)

MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories., Meyer, Tim, D’Abramo Marco, Hospital Adam, Rueda Manuel, Ferrer-Costa Carles, Pérez Alberto, Carrillo Oliver, Camps Jordi, Fenollosa Carles, Repchevsky Dmitry, et al. , Structure, 2010 Nov 10, Volume 18, p.1399-409, (2010)

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)

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)

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)

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA., Lavery, Richard, Zakrzewska Krystyna, Beveridge David, Bishop Thomas C., Case David A., Cheatham Thomas, Dixit Surjit, Jayaram B, Lankaš Filip, Laughton Charles, et al. , Nucleic Acids Res, 2010 Jan, Volume 38, p.299-313, (2010)

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA., Lavery, Richard, Zakrzewska Krystyna, Beveridge David, Bishop Thomas C., Case David A., Cheatham Thomas, Dixit Surjit, Jayaram B, Lankaš Filip, Laughton Charles, et al. , Nucleic Acids Res, 2010 Jan, Volume 38, p.299-313, (2010)

A hybrid all-atom/coarse grain model for multiscale simulations of DNA, Machado, Matías Rodrigo, Dans Pablo Daniel, and Pantano Sergio , Physical Chemistry Chemical Physics, Volume 13, Number 40, p.18134–18144, (2011)

Switching reversibility to irreversibility in glycogen synthase kinase 3 inhibitors: clues for specific design of new compounds, Perez, Daniel I., Palomo Valle, Pérez Concepción, Gil Carmen, Dans Pablo Daniel, F Luque Javier, Conde Santiago, and Martínez Ana , Journal of medicinal chemistry, Volume 54, Number 12, p.4042–4056, (2011)

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Pinyol Magda, Quesada Víctor, Conde Laura, Ordóñez Gonzalo R., Villamor Neus, Escaramis Georgia, Jares Pedro, Beà Sílvia, González-Díaz Marcos, et al. , Nature, 2011 Jul 7, Volume 475, p.101-5, (2011)

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Pinyol Magda, Quesada Víctor, Conde Laura, Ordóñez Gonzalo R., Villamor Neus, Escaramis Georgia, Jares Pedro, Beà Sílvia, González-Díaz Marcos, et al. , Nature, 2011 Jul 7, Volume 475, p.101-5, (2011)

Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations, Zeida, Ari, Machado Matías Rodrigo, Dans Pablo Daniel, and Pantano Sergio , Physical Review E, Volume 86, Number 2, p.021903, (2012)

Characterization of the impact of alternative splicing on protein dynamics: the cases of glutathione S-transferase and ectodysplasin-A isoforms., Barbany, Montserrat, Morata Jordi, Meyer Tim, Lois Sergi, Orozco Modesto, and de la Cruz Xavier , Proteins, 2012 Aug, Volume 80, p.2235-49, (2012)

Characterization of the impact of alternative splicing on protein dynamics: the cases of glutathione S-transferase and ectodysplasin-A isoforms., Barbany, Montserrat, Morata Jordi, Meyer Tim, Lois Sergi, Orozco Modesto, and de la Cruz Xavier , Proteins, 2012 Aug, Volume 80, p.2235-49, (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)

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)

Essential role of glutamate 317 in galactosyl transfer by α3GalT: a computational study., Gómez, Hansel, Lluch José M., and Masgrau Laura , Carbohydr Res, 2012 Jul 15, Volume 356, p.204-8, (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)

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)

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)

Ligand-induced formation of transient dimers of mammalian 12/15-lipoxygenase: a key to allosteric behavior of this class of enzymes?, Ivanov, Igor, Shang Weifeng, Toledo Lea, Masgrau Laura, Svergun Dmitri I., Stehling Sabine, Gómez Hansel, Di Venere Almerinda, Mei Giampiero, Lluch José M., et al. , Proteins, 2012 Mar, Volume 80, p.703-12, (2012)

Ligand-induced formation of transient dimers of mammalian 12/15-lipoxygenase: a key to allosteric behavior of this class of enzymes?, Ivanov, Igor, Shang Weifeng, Toledo Lea, Masgrau Laura, Svergun Dmitri I., Stehling Sabine, Gómez Hansel, Di Venere Almerinda, Mei Giampiero, Lluch José M., et al. , Proteins, 2012 Mar, Volume 80, p.703-12, (2012)

Retaining glycosyltransferase mechanism studied by QM/MM methods: lipopolysaccharyl-α-1,4-galactosyltransferase C transfers α-galactose via an oxocarbenium ion-like transition state., Gómez, Hansel, Polyak Iakov, Thiel Walter, Lluch José M., and Masgrau Laura , J Am Chem Soc, 2012 Mar 14, Volume 134, p.4743-52, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Structure-based identification of new high-affinity nucleosome binding sequences., Battistini, Federica, Hunter Christopher A., Moore Irene K., and Widom Jonathan , J Mol Biol, 2012 Jun 29, Volume 420, p.8-16, (2012)

Unveiling case-control relationships in designing a simple and powerful method for detecting gene-gene interactions., Canela-Xandri, Oriol, Julià Antonio, Gelpí Josep-Lluis, and Marsal Sara , Genet Epidemiol, 2012 Nov, Volume 36, p.710-6, (2012)

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)

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)

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)

DASiR: Distributed Annotation System in R, Flores, Oscar, and Mantsoki Anna , (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)