Biblio

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 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 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)

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)

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)

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)

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)

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)

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)

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)

BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows, Andrio, Pau, Hospital Adam, Conejero Javier, Jordá Luis, Del Pino Marc, Codó Laia, Soiland-Reyes Stian, Goble Carole, Lezzi Daniele, Badia Rosa M., et al. , Nature Scientific Data, 09/2019, Volume 6, Issue 1, p.169, (2019)

Bioactive Conformational Ensemble Server And Database. A Public Framework To Speed Up In Silico Drug Discovery, Zivanovic, Sanja, Bayarri Genis, Colizzi Francesco, Moreno David, Gelpí Josep Lluis, Soliva Robert, Hospital Adam, and Orozco Modesto , Journal of Chemical Theory and Computation, 08/2020, (2020)

Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent., Ortega, José-Antonio, Blas José Ramón, Orozco Modesto, Grandas Anna, Pedroso Enrique, and Robles Jordi , Org Lett, 2007 Oct 25, Volume 9, p.4503-6, (2007)

Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent., Ortega, José-Antonio, Blas José Ramón, Orozco Modesto, Grandas Anna, Pedroso Enrique, and Robles Jordi , Org Lett, 2007 Oct 25, Volume 9, p.4503-6, (2007)

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data., Hospital, Adam, Andrio Pau, Cugnasco Cesare, Codó Laia, Becerra Yolanda, Dans Pablo D., Battistini Federica, Torres Jordi, Goni Ramon, Orozco Modesto, et al. , Nucleic Acids Res, 2016 Jan 4, Volume 44, Issue D1, p.D272-8, (2016)

Benzoderivatives of nucleic acid bases as modified DNA building blocks., Huertas, Oscar, Blas José Ramón, Soteras Ignacio, Orozco Modesto, and F Luque Javier , J Phys Chem A, 2006 Jan 19, Volume 110, p.510-8, (2006)

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)

An atomistic view to the gas phase proteome., Meyer, Tim, de la Cruz Xavier, and Orozco Modesto , Structure, 2009 Jan 14, Volume 17, p.88-95, (2009)

An artificial DNAzyme RNA ligase shows a reaction mechanism resembling that of cellular polymerases, Aranda, Juan, Terrazas Montserrat, Gómez Hansel, Villegas Núria, and Orozco Modesto , Nature Catalysis, 06/2019, Volume 2, Issue 6, p.544 - 552, (2019)

Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study., Pérez, Alberto, Sponer Jiri, Jurecka Petr, Hobza Pavel, F Luque Javier, and Orozco Modesto , Chemistry, 2005 Aug 19, Volume 11, p.5062-6, (2005)

Approaching Elastic Network Models to Molecular Dynamics Flexibility, Orellana, Laura, Rueda Manuel, Ferrer-Costa Carles, Lopez-Blanco José Ramón, Chacón Pablo, and Orozco Modesto , Journal of Chemical Theory and Computation, Volume 6, p.2910-2923, (2010)

Approaching Elastic Network Models to Molecular Dynamics Flexibility, Orellana, Laura, Rueda Manuel, Ferrer-Costa Carles, Lopez-Blanco José Ramón, Chacón Pablo, and Orozco Modesto , Journal of Chemical Theory and Computation, Volume 6, p.2910-2923, (2010)

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)

Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives., Aviñó, Anna, Cubero Elena, González Carlos, Eritja Ramon, and Orozco Modesto , J Am Chem Soc, 2003 Dec 24, Volume 125, p.16127-38, (2003)

Alternative splicing of transcription factors’ genes: beyond the increase of proteome diversity., Talavera, David, Orozco Modesto, and de la Cruz Xavier , Comp Funct Genomics, 2009, p.905894, (2009)

Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species., Valenzuela, Abel, Talavera David, Orozco Modesto, and de la Cruz Xavier , J Mol Biol, 2004 Jan 9, Volume 335, p.495-502, (2004)

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)

Ab initio study of the structural, tautomeric, pairing, and electronic properties of seleno-derivatives of thymine., Vázquez-Mayagoitia, Alvaro, Huertas Oscar, Brancolini Giorgia, Migliore Agostino, Sumpter Bobby G., Orozco Modesto, F Luque Javier, Di Felice Rosa, and Fuentes-Cabrera Miguel , J Phys Chem B, 2009 Oct 29, Volume 113, p.14465-72, (2009)

Ab initio study of naphtho-homologated DNA bases., Vazquez-Mayagoita, Alvaro, Huertas Oscar, Fuentes-Cabrera Miguel, Sumpter Bobby G., Orozco Modesto, and F Luque Javier , J Phys Chem B, 2008 Feb 21, Volume 112, p.2179-86, (2008)

8-Amino guanine accelerates tetramolecular G-quadruplex formation., Gros, Julien, Aviñó Anna, de la Osa Jaime Lopez, González Carlos, Lacroix Laurent, Pérez Alberto, Orozco Modesto, Eritja Ramon, and Mergny Jean-Louis , Chem Commun (Camb), 2008 Jul 7, p.2926-8, (2008)

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence, Sati, Satish, Bonev Boyan, Szabo Quentin, Jost Daniel, Bensadoun Paul, Serra Francois, Loubiere Vincent, Papadopoulos Giorgio Lucio, Rivera-Mulia Juan-Carlos, Fritsch Lauriane, et al. , Molecular Cell, 07/2020, Volume 78, Issue 3, p.522 - 538.e9, (2020)

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)