Biblio

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)

Essential Dynamics: A Tool for Efficient Trajectory Compression and Management, Meyer, Tim, Ferrer-Costa Carles, Pérez Alberto, Rueda Manuel, Bidon-Chanal Axel, F. Luque Javier, Laughton Charles. A., and Orozco Modesto , Journal of Chemical Theory and Computation, 2006/03/01, Volume 2, Issue 2, p.251 - 258, (2006)

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 aberrant super-enhancer DNA methylation in human cancer, Heyn, Holger, Vidal Enrique, Ferreira Humberto J., Vizoso Miguel, Sayols Sergi, Gomez Antonio, Moran Sebastian, Boque-Sastre Raquel, Guil Sonia, Martinez-Cardus Anna, et al. , Genome Biology, 01/2016, Volume 17, p.11, (2016)

Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program, Janin, Maxime, Ortiz-Barahona Vanessa, de Moura Manuel Castro, Martinez-Cardus Anna, Llinàs-Arias Pere, Soler Marta, Nachmani Daphna, Pelletier Joffrey, Schumann Ulrike, Calleja-Cervantes Maria E., et al. , Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)

Enzyme-directed mutasynthesis: a combined experimental and theoretical approach to substrate recognition of a polyketide synthase., Sundermann, Uschi, Bravo-Rodriguez Kenny, Klopries Stephan, Kushnir Susanna, Gómez Hansel, Sanchez-Garcia Elsa, and Schulz Frank , ACS Chem Biol, 2013 Feb 15, Volume 8, p.443-50, (2013)

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)

Enabling HMMER for the Grid with COMP Superscalar, Tejedor, Enric, Badia Rosa M., Royo Romina, and Gelpí Josep-Lluis , Procedia Computer Science, Volume 1, p.2629–2638, (2010)

Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry, Sridhar, Akshay, Farr Stephen E., Portella Guillem, Schlick Tamar, Orozco Modesto, and Collepardo-Guevara Rosana , Proceedings of the National Academy of Sciences, 03/2020, Volume 117, Issue 13, p.7216, (2020)

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)

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)

Efficient siRNA-peptide conjugation for specific targeted delivery into tumor cells, Gandioso, Albert, Massaguer Anna, Villegas Núria, Salvans Cándida, Sanchez Dani, Brun-Heath Isabelle, Marchan Vicente, Orozco Modesto, and Terrazas Montserrat , Chemical Communications, 03/2017, Volume 53, Issue 19, p.2870 - 2873, (2017)

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)

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)

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)

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)

Effect of zinc and calcium ions on the rat kidney membrane-bound form of dipeptidyl peptidase IV., Gómez, Hansel, Chappé Mae, Valiente Pedro A., Pons Tirso, Chávez María de Los Ang, Charli Jean-Louis, and Pascual Isel , J Biosci, 2013 Sep, Volume 38, p.461-9, (2013)

Effect of divalent cations on the porcine kidney cortex membrane-bound form of dipeptidyl peptidase IV., Pascual, Isel, Gómez Hansel, Pons Tirso, Chappé Mae, Vargas Miguel Angel, Valdés Gilberto, Lopéz Alí, Saroyán Angélika, Charli Jean-Louis, and Chávez María de los Ang , Int J Biochem Cell Biol, 2011 Mar, Volume 43, p.363-71, (2011)

Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct., Gómez-Pinto, Irene, Cubero Elena, Kalko Susana G., Monaco Vania, van der Marel Gijs, van Boom Jacques H., Orozco Modesto, and González Carlos , J Biol Chem, 2004 Jun 4, Volume 279, p.24552-60, (2004)

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)

Dynamics of B-DNA on the microsecond time scale., Pérez, Alberto, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2007 Nov 28, Volume 129, p.14739-45, (2007)

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)

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)

DNA-triplex stabilizing properties of 8-aminoguanine, Soliva, Robert, García Ramón Güimil, J. Blas Ramón, Eritja Ramon, Asensio Juan Luis, González Carlos, F. Luque Javier, and Orozco Modesto , Nucleic Acids Research, Volume 28, p.4531-4539, (2000)

DNAlive: a tool for the physical analysis of DNA at the genomic scale., J Goñi, Ramon, Fenollosa Carlos, Pérez Alberto, Torrents David, and Orozco Modesto , Bioinformatics, 2008 Aug 1, Volume 24, p.1731-2, (2008)

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)

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)

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)

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)

A DNA methylation map of human cancer at single base-pair resolution, Vidal, E, Sayols S, Moran S, Guillaumet-Adkins A, Schroeder M P., Royo R, Orozco Modesto, Gut M, Gut I, Lopez-Bigas N, et al. , Oncogene, 06/2017, p.1-10, (2017)

DNA double-strand break-derived RNA drives TIRR/53BP1 complex dissociation, Ketley, Ruth F., Battistini Federica, Alagia Adele, Mondielli Clémence, Iehl Florence, Balikçi Esra, Huber Kilian V. M., Orozco Modesto, and Gullerova Monika , Cell Reports, 10/2022, Volume 41, Issue 4, (2022)

Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family., Soliva, Robert, Gelpí Josep-Lluis, Almansa Carmen, Virgili Marina, and Orozco Modesto , J Med Chem, 2007 Jan 25, Volume 50, p.283-93, (2007)

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)

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)

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)

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)

DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs, Moreno, David, Zivanovic Sanja, Colizzi Francesco, Hospital Adam, Aranda Juan, Soliva Robert, and Orozco Modesto , Journal of Chemical Theory and Computation, 08/2020, (2020)

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew, Bergsma Johan, Merkys Andrius, Andersen Casper, Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, p. - , (2024)

Determining promoter location based on DNA structure first-principles calculations., J Goñi, Ramon, Pérez Alberto, Torrents David, and Orozco Modesto , Genome Biol, 2007, Volume 8, p.R263, (2007)

Determination of a Structural Ensemble Representing the Dynamics of a G-Quadruplex DNA, Portella, Guillem, Orozco Modesto, and Vendruscolo Michele , Biochemistry, 12/2019, (2019)

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)

Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer’s disease., Muñoz-Ruiz, Pilar, Rubio Laura, García-Palomero Esther, Dorronsoro Isabel, del Monte-Millán María, Valenzuela Rita, Usán Paola, de Austria Celia, Bartolini Manuela, Andrisano Vincenza, et al. , J Med Chem, 2005 Nov 17, Volume 48, p.7223-33, (2005)

Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels., Portella, Guillem, Polupanow Tanja, Zocher Florian, Boytsov Danila A., Pohl Peter, Diederichsen Ulf, and de Groot Bert L. , Biophys J, 2012 Oct 17, Volume 103, p.1698-705, (2012)

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)

A deletion at ADAMTS9-MAGI1 locus is associated with psoriatic arthritis risk., Julià, Antonio, Pinto José Antonio, Gratacós Jordi, Queiró Rubén, Ferrándiz Carlos, Fonseca Eduardo, Montilla Carlos, Torre-Alonso Juan Carlos, Puig Lluís, Venegas José Javier Pé, et al. , Ann Rheum Dis, 2015 Oct, Volume 74, p.1875-81, (2015)

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)

Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease, Hernández-Alvarez, María Isabel, Sebastián David, Vives Sara, Ivanova Saška, Bartoccioni Paola, Kakimoto Pamela, Plana Natalia, Veiga Sónia R., Hernández Vanessa, Vasconcelos Nuno, et al. , Cell, 05/2019, Volume 177, Issue 4, p.881 - 895.e17, (2019)

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)

Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily., Raimondi, Francesco, Orozco Modesto, and Fanelli Francesca , Structure, 2010 Mar 10, Volume 18, p.402-14, (2010)