Biblio

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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 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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

De novo design of a non-local β-sheet protein with high stability and accuracy, Marcos, Enrique, Chidyausiku Tamuka M., McShan Andrew C., Evangelidis Thomas, Nerli Santrupti, Carter Lauren, Nivón Lucas G., Davis Audrey, Oberdorfer Gustav, Tripsianes Konstantinos, et al. , Nature structural & molecular biology, 11/2018, Volume 25, Issue 11, p.1028 - 1034, (2018)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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 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)

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)

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-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)

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)

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 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 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)