Biblio

Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH, Portella, Guillem, Terrazas Montserrat, Villegas Núria, González Carlos, and Orozco Modesto , Angewandte Chemie International Edition, Volume 54, p.10488–10491, (2015)

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)

Challenges and guidelines toward 4D nucleome data and model standards, Marti-Renom, Marc A., Almouzni Genevieve, Bickmore Wendy A., Bystricky Kerstin, Cavalli Giacomo, Fraser Peter, Gasser Susan M., Giorgetti Luca, Heard Edith, Nicodemi Mario, et al. , Nature Genetics, 10/2018, Volume 50, Issue 10, p.1352 - 1358, (2018)

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations, Kuzmanic, Antonija, Sutto Ludovico, Saladino Giorgio, Nebreda Angel R., Gervasio Francesco L., and Orozco Modesto , eLife, 04/2017, Volume 6, p.e22175, (2017)

Chapter 7 Molecular Modelling of Nucleic Acids, Gómez, Hansel, Walther Jurgen, Darré Leonardo, Ivani Ivan, Dans Pablo D., and Orozco Modesto , Computational Tools for Chemical Biology, p.165 - 197, (2017)

Characterization of compensated mutations in terms of structural and physico-chemical properties., Ferrer-Costa, Carles, Orozco Modesto, and de la Cruz Xavier , J Mol Biol, 2007 Jan 5, Volume 365, p.249-56, (2007)

Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties., Ferrer-Costa, Carles, Orozco Modesto, and de la Cruz Xavier , J Mol Biol, 2002 Jan 25, Volume 315, p.771-86, (2002)

Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway, González, Lorena, Díaz Lucía, Pous Joan, Baginski Blazej, Duran-Corbera Anna, Scarpa Margherita, Brun-Heath Isabelle, Igea Ana, Martin-Malpartida Pau, Ruiz Lidia, et al. , Nature Communications, 06/2023, Volume 14, Issue 1, p.3318, (2023)

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)

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)

Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins., Gelpí, Josep-Lluis, Kalko S G., Barril X, Cirera J, de La Cruz X, Luque F J., and Orozco Modesto , Proteins, 2001 Dec 1, Volume 45, p.428-37, (2001)

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)

Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings., Orozco, Modesto, Orellana Laura, Hospital Adam, Naganathan Athi N., Emperador Agustí, Carrillo Oliver, and Gelpí J L. , Adv Protein Chem Struct Biol, 2011, Volume 85, p.183-215, (2011)

COCO: a simple tool to enrich the representation of conformational variability in NMR structures., Laughton, Charles A., Orozco Modesto, and Vranken Wim , Proteins, 2009 Apr, Volume 75, p.206-16, (2009)

Colibactin DNA-damage signature indicates mutational impact in colorectal cancer, Dziubańska-Kusibab, Paulina J., Berger Hilmar, Battistini Federica, Bouwman Britta A. M., Iftekhar Amina, Katainen Riku, Cajuso Tatiana, Crosetto Nicola, Orozco Modesto, Aaltonen Lauri A., et al. , Nature Medicine, 07/2020, Volume 26, Issue 7, p.1063 - 1069, (2020)

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community), Orengo, C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, et al. , F1000Research, 04/2020, Volume 9, (2020)

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry, Porrini, Massimiliano, Rosu Frédéric, Rabin Clémence, Darré Leonardo, Gómez Hansel, Orozco Modesto, and Gabelica Valérie , ACS Central Science, 05/2017, Volume 3, Issue 5, p.454 - 461, (2017)

Comparison of molecular dynamics and superfamily spaces of protein domain deformation., Velázquez-Muriel, Javier A., Rueda Manuel, Cuesta Isabel, Pascual-Montano Alberto, Orozco Modesto, and Carazo José-María , BMC Struct Biol, 2009, Volume 9, p.6, (2009)

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)

A computational and experimental study of O-glycosylation. Catalysis by human UDP-GalNAc polypeptide:GalNAc transferase-T2., Gómez, Hansel, Rojas Raúl, Patel Divya, Tabak Lawrence A., Lluch José M., and Masgrau Laura , Org Biomol Chem, 2014 May 7, Volume 12, p.2645-55, (2014)

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)

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)

Connecting proline and γ-aminobutyric acid in stressed plants through non-enzymatic reactions., Signorelli, Santiago, Dans Pablo D., E Coitiño Laura, Borsani Omar, and Monza Jorge , PLoS One, 2015, Volume 10, p.e0115349, (2015)

A consensus view of protein dynamics., Rueda, Manuel, Ferrer-Costa Carles, Meyer Tim, Pérez Alberto, Camps Jordi, Hospital Adam, Gelpí Josep-Lluis, and Orozco Modesto , Proc Natl Acad Sci U S A, 2007 Jan 16, Volume 104, p.796-801, (2007)

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)

Continuum and discrete calculation of fractional contributions to solvation free energy., Morreale, Antonio, Gelpí Josep-Lluis, F Luque Javier, and Orozco Modesto , J Comput Chem, 2003 Oct, Volume 24, p.1610-23, (2003)

Contribution of engineered electrostatic interactions to the stability of cytosolic malate dehydrogenase., Trejo, F, Gelpí Josep-Lluis, Ferrer A, Boronat A, Busquets M, and Cortés A , Protein Eng, 2001 Nov, Volume 14, p.911-7, (2001)

Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides, Genna, Vito, Iglesias-Fernández Javier, Reyes-Fraile Laura, Villegas Núria, Guckian Kevin, Seth Punit, Wan Brad, Cabrero Cristina, Terrazas Montserrat, Brun-Heath Isabelle, et al. , Nucleic Acids Research, 06/2023, Volume 51, Issue 10, p.4713 - 4725, (2023)

Cooperativity in Drug-DNA Recognition: A Molecular Dynamics Study, Harris, Sarah A., Gavathiotis Evripidis, Searle Mark S., Orozco Modesto, and Laughton Charles A. , Journal of the American Chemical Society, 2001/12/01, Volume 123, Issue 50, p.12658 - 12663, (2001)

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 in DNA: beyond base-pair step models of DNA flexibility, López-Güell, Kim, Battistini Federica, and Orozco Modesto , Nucleic Acids Research, 06/2023, Volume 51, Issue 6, p.2633 - 2640, (2023)

Cystinuria-specific rBAT(R365W) mutation reveals two translocation pathways in the amino acid transporter rBAT-b0,+AT., Pineda, Marta, Wagner Carsten A., Bröer Angelika, Stehberger Paul A., Kaltenbach Simone, Gelpí Josep-Lluis, Del Río Rafael Martín, Zorzano Antonio, Palacín Manuel, Lang Florian, et al. , Biochem J, 2004 Feb 1, Volume 377, p.665-74, (2004)