Biblio

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)

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?, da Rosa, Gabriela, Grille Leandro, Calzada Victoria, Ahmad Katya, Arcon Juan Pablo, Battistini Federica, Bayarri Genis, Bishop Thomas, Carloni Paolo, III Thomas Cheatham, et al. , Biophysical Reviews, 11/2021, (2021)

Electrostatic component of solvation: comparison of SCRF continuum models., Curutchet, Carles, Cramer Christopher J., Truhlar Donald G., Ruiz-López Manuel F., Rinaldi Daniel, Orozco Modesto, and F Luque Javier , J Comput Chem, 2003 Feb, Volume 24, p.284-97, (2003)

Transferability of fragmental contributions to the octanol/water partition coefficient: an NDDO-based MST study., Curutchet, C, Salichs A, Barril X, Orozco Modesto, and F Luque Javier , J Comput Chem, 2003 Jan 15, Volume 24, p.32-45, (2003)

Dispersion and repulsion contributions to the solvation free energy: comparison of quantum mechanical and classical approaches in the polarizable continuum model., Curutchet, Carles, Orozco Modesto, F Luque Javier, Mennucci Benedetta, and Tomasi Jacopo , J Comput Chem, 2006 Nov 30, Volume 27, p.1769-80, (2006)

MST continuum study of the hydration free energies of monovalent ionic species., Curutchet, Carles, Bidon-Chanal Axel, Soteras Ignaci, Orozco Modesto, and F Luque Javier , J Phys Chem B, 2005 Mar 3, Volume 109, p.3565-74, (2005)

Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations., Curutchet, Carles, Bofill Josep María, Hernández Begoña, Orozco Modesto, and F Luque Javier , J Comput Chem, 2003 Jul 30, Volume 24, p.1263-75, (2003)

DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region, Cuppari, Anna, Fernández-Millán Pablo, Battistini Federica, Tarrés-Solé Aleix, Lyonnais Sébastien, Iruela Guillermo, Ruiz-López Elena, Enciso Yuliana, Rubio-Cosials Anna, Prohens Rafel, et al. , Nucleic acids research, 09/2019, Volume 47, Issue 12, p.6519 - 6537, (2019)

Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop, Cunha, Eva S., Sfriso Pedro, Rojas Adriana L., Hospital Adam, Orozco Modesto, and Abrescia Nicola G. A. , Structure, 01/2017, Volume 25, p.53-65, (2017)

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 effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine, Cubero, Elena, Güimil-García Ramon, F. Luque Javier, Eritja Ramon, and Orozco Modesto , Nucleic Acids Research, Volume 29, p.2522-2534, (2001)

Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA., Cubero, Elena, F Luque Javier, and Orozco Modesto , Biophys J, 2006 Feb 1, Volume 90, p.1000-8, (2006)

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)

RNA dynamics from experimental and computational approaches, Bussi, Giovanni, Bonomi Massimiliano, Gkeka Paraskevi, Sattler Michael, Al-Hashimi Hashim M., Auffinger Pascal, Duca Maria, Foricher Yann, Incarnato Danny, Jones Alisha N., et al. , Structure, 09/2024, Volume 32, Issue 9, p.1281 - 1287, (2024)

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)

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)

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)

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)

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows, Bayarri, Genis, Andrio Pau, Gelpí Josep Lluis, Hospital Adam, and Orozco Modesto , PLOS Computational Biology, 06/2024, Volume 20, Issue 6, p.e1012173 , (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)

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)

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)

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)