Biblio

Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives., Cubero, Elena, Aviñó Anna, de la Torre Beatriz G., Frieden Miriam, Eritja Ramon, F Luque Javier, González Carlos, and Orozco Modesto , J Am Chem Soc, 2002 Mar 27, Volume 124, p.3133-42, (2002)

Molecular Dynamics Study of Oligonucleotides Containing Difluorotoluene, Cubero, Elena, Laughton Charles A., F. Luque Javier, and Orozco Modesto , Journal of the American Chemical Society, Volume 122, p.6891-6899, (2000)

Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex., Cubero, Elena, Abrescia Nicola G. A., Subirana Juan A., F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2003 Nov 26, Volume 125, p.14603-12, (2003)

Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism., Crespo, Alejandro, Martí Marcelo A., Kalko Susana G., Morreale Antonio, Orozco Modesto, Gelpí Josep-Lluis, F Luque Javier, and Estrin Darío A. , J Am Chem Soc, 2005 Mar 30, Volume 127, p.4433-44, (2005)

Target flexibility: an emerging consideration in drug discovery and design., Cozzini, Pietro, Kellogg Glen E., Spyrakis Francesca, Abraham Donald J., Costantino Gabriele, Emerson Andrew, Fanelli Francesca, Gohlke Holger, Kuhn Leslie A., Morris Garrett M., et al. , J Med Chem, 2008 Oct 23, Volume 51, p.6237-55, (2008)

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes., Conde, Lucía, Vaquerizas Juan M., Ferrer-Costa Carles, de la Cruz Xavier, Orozco Modesto, and Dopazo Joaquin , Nucleic Acids Res, 2005 Jul 1, Volume 33, p.W501-5, (2005)

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study, Collepardo-Guevara, Rosana, Portella Guillem, Vendruscolo Michele, Frenkel Daan, Schlick Tamar, and Orozco Modesto , Journal of the American Chemical Society, 2015/08/19, Volume 137, Issue 32, p.10205 - 10215, (2015)

Probing allosteric regulations with coevolution-driven molecular simulations, Colizzi, Francesco, and Orozco Modesto , Science advances, 10/2021, Volume 7, Issue 37, p.eabj0786 - eabj0786, (2021)

Predicting the limit of intramolecular H-Bonding with classical molecular dynamics, Colizzi, Francesco, Hospital Adam, Zivanovic Sanja, and Orozco Modesto , Angewandte Chemie International Edition, 01/2019, (2019)

Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design, Chaudhuri, Rima, Carrillo Oliver, Laughton Charles A., and Orozco Modesto , Journal of Chemical Theory and Computation, 2012/00/10, Volume 8, p.2204 - 2214, (2012)

DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p, Chakraborty, Arka, Lyonnais Sébastien, Battistini Federica, Hospital Adam, Medici Giorgio, Prohens Rafel, Orozco Modesto, Vilardell Josep, and Solà Maria , Nucleic Acids Research, 11/2016, (2016)

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)

Modulation of drug cytotoxicity by reintroduction of wild-type p53 gene (Ad5CMV-p53) in human pancreatic cancer., Cascalló, M, Calbó J, Gelpí J L., and Mazo A , Cancer Gene Ther, 2000 Apr, Volume 7, p.545-56, (2000)

GRID-MD-A tool for massive simulation of protein channels., Carrillo, Oliver, and Orozco Modesto , Proteins, 2008 Feb 15, Volume 70, p.892-9, (2008)

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)

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)

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)

FlexServ: an integrated tool for the analysis of protein flexibility., Camps, Jordi, Carrillo Oliver, Emperador Agustí, Orellana Laura, Hospital Adam, Rueda Manuel, Cicin-Sain Damjan, D’Abramo Marco, Gelpí Josep-Lluis, and Orozco Modesto , Bioinformatics, 2009 Jul 1, Volume 25, p.1709-10, (2009)

Adenovirus-mediated wt-p16 reintroduction induces cell cycle arrest or apoptosis in pancreatic cancer., Calbó, J, Marotta M, Cascalló M, Roig J M., Gelpí Josep-Lluis, Fueyo J, and Mazo A , Cancer Gene Ther, 2001 Oct, Volume 8, p.740-50, (2001)

Glutaryl-CoA dehydrogenase deficiency in Spain: evidence of two groups of patients, genetically, and biochemically distinct., Busquets, C, Merinero B, Christensen E, Gelpí Josep-Lluis, Campistol J, Pineda M, Fernández-Alvarez E, Prats J M., Sans A, Arteaga R, et al. , Pediatr Res, 2000 Sep, Volume 48, p.315-22, (2000)

Impact of DNA methylation on 3D genome structure, Buitrago, Diana, Labrador Mireia, Arcon Juan Pablo, Lema Rafael, Flores Oscar, Esteve-Codina Anna, Blanc Julie, Villegas Núria, Bellido David, Gut Marta, et al. , Nature Communications, 05/2021, Volume 12, Issue 1, p.3243, (2021)

Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning, Buitrago, Diana, Codó Laia, Illa Ricard, de Jorge Pau, Battistini Federica, Flores Oscar, Bayarri Genis, Royo Romina, Del Pino Marc, Heath Simon, et al. , Nucleic Acids Research, 08/2019, (2019)

Theoretical study of anion binding to calix[4]pyrrole: the effects of solvent, fluorine substitution, cosolute, and water traces., J Blas, Ramón, Márquez Manuel, Sessler Jonathan L., F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2002 Oct 30, Volume 124, p.12796-805, (2002)

Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution., J Blas, Ramón, López-Bes Jose Maria, Márquez Manuel, Sessler Jonathan L., F Luque Javier, and Orozco Modesto , Chemistry, 2007, Volume 13, p.1108-16, (2007)

Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases., Blas, José Ramón, Huertas Oscar, Tabares Carolina, Sumpter Bobby G., Fuentes-Cabrera Miguel, Orozco Modesto, Ordejón Pablo, and F Luque Javier , J Phys Chem A, 2011 Oct 20, Volume 115, p.11344-54, (2011)

Unique tautomeric properties of isoguanine., Blas, José Ramón, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2004 Jan 14, Volume 126, p.154-64, (2004)

Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N., Bidon-Chanal, Axel, Martí Marcelo A., Crespo Alejandro, Milani Mario, Orozco Modesto, Bolognesi Martino, F Luque Javier, and Estrin Darío A. , Proteins, 2006 Aug 1, Volume 64, p.457-64, (2006)

Solvation enthalpies of neutral solutes in water and octanol, Bidon-Chanal, Axel, Huertas Oscar, Orozco Modesto, and F Luque Javier , Theoretical Chemistry Accounts, 2009/05/01, Volume 123, p.11-20, (2009)

Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair., Beuning, Penny J., Nagan Maria C., Cramer Christopher J., Musier-Forsyth Karin, Gelpí Josep-Lluis, and Bashford Donald , RNA, 2002 May, Volume 8, p.659-70, (2002)

A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort, Beltrán, Daniel, Hospital Adam, Gelpí Josep Lluis, and Orozco Modesto , Nucleic Acids Res, 04/2024, Volume 52, Issue D1, p.D393 - D403, (2024)

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations, Bayarri, Genis, Andrio Pau, Hospital Adam, Orozco Modesto, and Gelpí Josep Lluís , Nucleic Acids Res, 05/2022, Volume 50, Issue W1, p.W107, (2022)

3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories, Bayarri, Genis, Hospital Adam, and Orozco Modesto , Frontiers in Molecular Biosciences, 08/2021, Volume 8, p.795, (2021)

BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools, Bayarri, Genis, Andrio Pau, Hospital Adam, Orozco Modesto, and Gelpí Josep Lluis , Bioinformatics, 05/2022, Volume 38, Issue 12, p.3303, (2022)

Structural mechanics of DNA wrapping in the nucleosome., Battistini, Federica, Hunter Christopher A., Gardiner Eleanor J., and Packer Martin J. , J Mol Biol, 2010 Feb 19, Volume 396, p.264-79, (2010)

A commentary on the ABC consortium and its impact on the development of mesoscopic models of DNA, Battistini, Federica , Biophysical Reviews, 04/2024, (2024)

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition, Battistini, Federica, Hospital Adam, Buitrago Diana, Gallego Diego, Dans Pablo D., Gelpí Josep Lluis, and Orozco Modesto , Journal of Molecular Biology, 07/2019, (2019)

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)

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function, Battistini, Federica, Dans Pablo D., Terrazas Montserrat, Castellazzi Chiara L., Portella Guillem, Labrador Mireia, Villegas Núria, Brun-Heath Isabelle, González Carlos, and Orozco Modesto , PLOS Computational Biology, 11/2021, Volume 17, Issue 11, p.e1009547 - , (2021)

Sequence-Dependent Properties of the RNA Duplex, Battistini, Federica, Sala Alba, Hospital Adam, and Orozco Modesto , Journal of Chemical Information and Modeling, 08/2023, Volume 63, Issue 16, p.5259 - 5271, (2023)

Deciphering the mechanical code of the genome and epigenome, Basu, Aakash, Bobrovnikov Dmitriy G., Cieza Basilio, Arcon Juan Pablo, Qureshi Zan, Orozco Modesto, and Ha Taekjip , Nat Struct Mol Biol, 12/2022, Volume 29, Issue 12, p.1178 - 1187, (2022)

DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors, Barissi, Sandro, Sala Alba, Wieczór Miłosz, Battistini Federica, and Orozco Modesto , Nucleic Acids Res, 09/2022, Volume 50, Issue 16, (2022)

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)

Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins, Barbany, Montserrat, Meyer Tim, Hospital Adam, Faustino Ignacio, D’Abramo Marco, Morata Jordi, Orozco Modesto, and de la Cruz Xavier , PLoS ONE, 2015/03/27, Volume 10, p.e0119978 -, (2015)

Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond, Balaceanu, Alexandra, Buitrago Diana, Walther Jurgen, Hospital Adam, Dans Pablo D., and Orozco Modesto , 01/2019, (2019)

Allosterism and signal transfer in DNA, Balaceanu, Alexandra, Pérez Alberto, Dans Pablo D., and Orozco Modesto , Nucleic Acids Research, 2018/09/06, Volume 46, Issue 15, p.7554 - 7565, (2018)

The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA, Balaceanu, Alexandra, Pasi Marco, Dans Pablo D., Hospital Adam, Lavery Richard, and Orozco Modesto , The Journal of Physical Chemistry Letters, 01/01/2017, Volume 8, p.21 - 28, (2017)

Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering., Ayuso-Tejedor, Sara, García-Fandiño Rebeca, Orozco Modesto, Sancho Javier, and Bernadó Pau , J Mol Biol, 2011 Mar 4, Volume 406, p.604-19, (2011)

Structural properties of g,t-parallel duplexes., Aviñó, Anna, Cubero Elena, Gargallo Raimundo, González Carlos, Orozco Modesto, and Eritja Ramon , J Nucleic Acids, 2010, Volume 2010, (2010)

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)

Triplex formation using oligonucleotide clamps carrying 8-aminopurines., Aviñó, Anna, Grimau Marta G., Alvira Margarita, Eritja Ramon, Gargallo Raimundo, Orozco Modesto, and González Carlos , Nucleosides Nucleotides Nucleic Acids, 2007, Volume 26, p.979-83, (2007)