Biblio

The structural impact of DNA mismatches., Rossetti, Giulia, Dans Pablo D., Gómez-Pinto Irene, Ivani Ivan, González Carlos, and Orozco Modesto , Nucleic Acids Res, 2015 Apr 30, Volume 43, p.4309-21, (2015)

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance, Pluta, Radoslaw, D. Boer Roeland, Lorenzo-Díaz Fabián, Russi Silvia, Gómez Hansel, Fernández-López Cris, Pérez-Luque Rosa, Orozco Modesto, Espinosa Manuel, and Coll Miquel , Proc. Natl. Acad. Sci, USA, 08/2017, Volume 114, Issue 32, p.E6526 - E6535, (2017)

Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism, Tarrés-Solé, Aleix, Battistini Federica, Gerhold Joachim M., Piétrement Olivier, Martínez-García Belén, Ruiz-López Elena, Lyonnais Sébastien, Bernadó Pau, Roca Joaquim, Orozco Modesto, et al. , Nucleic Acids Research, 05/2023, p.gkad397, (2023)

Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering., Ayuso-Tejedor, Sara, García-Fandiño Rebeca, Orozco Modesto, Sancho Javier, and Bernadó Pau , J Mol Biol, 2011 Mar 4, Volume 406, p.604-19, (2011)

Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures., Aviñó, Anna, Portella Guillem, Ferreira Ruben, Gargallo Raimundo, Mazzini Stefania, Gabelica Valérie, Orozco Modesto, and Eritja Ramon , FEBS J, 2014 Feb, Volume 281, p.1085-99, (2014)

Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures., Aviñó, Anna, Portella Guillem, Ferreira Ruben, Gargallo Raimundo, Mazzini Stefania, Gabelica Valérie, Orozco Modesto, and Eritja Ramon , FEBS J, 2014 Feb, Volume 281, p.1085-99, (2014)

Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety, Soliva, R., Monaco V., Gómez-Pinto I., Meeuwenoord N. J., Van der Marel G. A., Van Boom J. H., González C., and Orozco Modesto , Nucleic Acids Research, Volume 29, p.2973-2985, (2001)

Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety, Soliva, R., Monaco V., Gómez-Pinto I., Meeuwenoord N. J., Van der Marel G. A., Van Boom J. H., González C., and Orozco Modesto , Nucleic Acids Research, Volume 29, p.2973-2985, (2001)

Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA, Darré, Leonardo, Ivani Ivan, Dans Pablo D., Gómez Hansel, Hospital Adam, and Orozco Modesto , Journal of the American Chemical Society, 12/2016, Volume 138, Issue 50, p.16355 - 16363, (2016)

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor, Escobedo, Albert, Topal Busra, Kunze Micha B. A., Aranda Juan, Chiesa Giulio, Mungianu Daniele, Bernardo-Seisdedos Ganeko, Eftekharzadeh Bahareh, Gairí Margarida, Pierattelli Roberta, et al. , Nature Communication, 05/2019, Volume 10, Issue 1, p.2034, (2019)

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor, Escobedo, Albert, Topal Busra, Kunze Micha B. A., Aranda Juan, Chiesa Giulio, Mungianu Daniele, Bernardo-Seisdedos Ganeko, Eftekharzadeh Bahareh, Gairí Margarida, Pierattelli Roberta, et al. , Nature Communication, 05/2019, Volume 10, Issue 1, p.2034, (2019)

Sequential amino acid exchange across b(0,+)-like system in chicken brush border jejunum., Torras-Llort, M, Torrents D, Soriano-García J F., Gelpí J L., Estévez R, Ferrer R, Palacín M, and Moretó M , J Membr Biol, 2001 Apr 1, Volume 180, p.213-20, (2001)

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)

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)

SEABED: Small molEcule activity scanner weB servicE baseD., Fenollosa, Carlos, Otón Marcel, Andrio Pau, Cortés Jorge, Orozco Modesto, and J Goñi Ramon , Bioinformatics, 2015 Mar 1, Volume 31, p.773-5, (2015)

Screening of inhibitors of porcine dipeptidyl peptidase IV activity in aqueous extracts from marine organisms, Pascual, Isel, Lopéz Alí, Gómez Hansel, Chappé Mae, Saroyán Angélika, Gonzalez Yamile, Cisneros Miguel, Charli Jean Louis, and Chávez María de los Ang , Enzyme Microb. Technol., Volume 40, Number {3, SI}, {360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA}, p.414-419, (2007)

Screening of inhibitors of porcine dipeptidyl peptidase IV activity in aqueous extracts from marine organisms, Pascual, Isel, Lopéz Alí, Gómez Hansel, Chappé Mae, Saroyán Angélika, Gonzalez Yamile, Cisneros Miguel, Charli Jean Louis, and Chávez María de los Ang , Enzyme Microb. Technol., Volume 40, Number {3, SI}, {360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA}, p.414-419, (2007)

SAR and 3D-QSAR studies on thiadiazolidinone derivatives: exploration of structural requirements for glycogen synthase kinase 3 inhibitors., Martínez, Ana, Alonso Mercedes, Castro Ana, Dorronsoro Isabel, Gelpí Josep-Lluis, F Luque Javier, Pérez Concepción, and Moreno Francisco J. , J Med Chem, 2005 Nov 17, Volume 48, p.7103-12, (2005)

Role of Pre-A motif in nitric oxide scavenging by truncated hemoglobin, HbN, of Mycobacterium tuberculosis., Lama, Amrita, Pawaria Sudesh, Bidon-Chanal Axel, Anand Arvind, Gelpí Josep-Lluis, Arya Swati, Martí Marcelo, Estrin Darío A., F Luque Javier, and Dikshit Kanak L. , J Biol Chem, 2009 May 22, Volume 284, p.14457-68, (2009)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Retaining glycosyltransferase mechanism studied by QM/MM methods: lipopolysaccharyl-α-1,4-galactosyltransferase C transfers α-galactose via an oxocarbenium ion-like transition state., Gómez, Hansel, Polyak Iakov, Thiel Walter, Lluch José M., and Masgrau Laura , J Am Chem Soc, 2012 Mar 14, Volume 134, p.4743-52, (2012)

QM/MM Studies Reveal How Substrate–Substrate and Enzyme–Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism, Gómez, Hansel, Mendoza Fernanda, Lluch José M., and Masgrau Laura , Advances in Protein Chemistry and Structural Biology, Volume 100, p.-, (2015)

QM/MM Studies Reveal How Substrate–Substrate and Enzyme–Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism, Gómez, Hansel, Mendoza Fernanda, Lluch José M., and Masgrau Laura , Advances in Protein Chemistry and Structural Biology, p.-, (2015)

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data, Shkurti, Ardita, Goni Ramon, Andrio Pau, Breitmoser Elena, Bethune Iain, Orozco Modesto, and Laughton Charles A. , SoftwareX, 12/2016, Volume 5, p.44 - 50, (2016)

Proton Dynamics in Protein Mass Spectrometry, Li, Jinyu, Lyu Wenping, Rossetti Giulia, Konijnenberg Albert, Natalello Antonino, Ippoliti Emiliano, Orozco Modesto, Sobott Frank, Grandori Rita, and Carloni Paolo , The Journal of Physical Chemistry Letters, 03/2017, Volume 8, Issue 6, p.1105 - 1112, (2017)

Proteins in the gas phase, Meyer, Tim, Gabelica Valérie, Grubmüller Helmut, and Orozco Modesto , WIREs Computational Molecular Science, Volume 3, p.408-425, (2013)

Proteins in the gas phase, Meyer, Tim, Gabelica Valérie, Grubmüller Helmut, and Orozco Modesto , WIREs Computational Molecular Science, Volume 3, p.408-425, (2013)

Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution, Rubio-Cosials, Anna, Battistini Federica, Gansen Alexander, Cuppari Anna, Bernadó Pau, Orozco Modesto, Langowski Jörg, Tóth Katalin, and Solà Maria , Biophysical Journal, 05/2018, Volume 114, p.2386 - 2396, (2018)

Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines., Aviñó, Anna, Frieden Miriam, Morales Juan Carlos, de la Torre Beatriz García, García Ramón Güimil, Azorín Ferran, Gelpí Josep-Lluis, Orozco Modesto, González Carlos, and Eritja Ramon , Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)

Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines., Aviñó, Anna, Frieden Miriam, Morales Juan Carlos, de la Torre Beatriz García, García Ramón Güimil, Azorín Ferran, Gelpí Josep-Lluis, Orozco Modesto, González Carlos, and Eritja Ramon , Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)

Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines., Aviñó, Anna, Frieden Miriam, Morales Juan Carlos, de la Torre Beatriz García, García Ramón Güimil, Azorín Ferran, Gelpí Josep-Lluis, Orozco Modesto, González Carlos, and Eritja Ramon , Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)

Principles for designing proteins with cavities formed by curved β sheets, Marcos, Enrique, Basanta Benjamin, Chidyausiku Tamuka M., Tang Yuefeng, Oberdorfer Gustav, Liu Gaohua, Swapna G V. T., Guan Rongjin, Silva Daniel-Adriano, Dou Jiayi, et al. , Science (New York, N.Y.), 01/2017, Volume 355, Issue 6321, p.201 - 206, (2017)

Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH, Mir, Bartomeu, Serrano Israel, Buitrago Diana, Orozco Modesto, Escaja Núria, and González Carlos , Journal of the American Chemical Society, 11/2017, Volume 139, Issue 40, p.13985 - 13988, (2017)

Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case, Wieczór, Miłosz, Genna Vito, Aranda Juan, Badia Rosa M., Gelpí Josep Lluis, Gapsys Vytautas, de Groot Bert L., Lindahl Erik, Municoy Martí, Hospital Adam, et al. , WIREs Computational Molecular Science, 05/2022, Volume In Press, p.e1622, (2022)

Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case, Wieczór, Miłosz, Genna Vito, Aranda Juan, Badia Rosa M., Gelpí Josep Lluis, Gapsys Vytautas, de Groot Bert L., Lindahl Erik, Municoy Martí, Hospital Adam, et al. , WIREs Computational Molecular Science, 05/2022, Volume In Press, p.e1622, (2022)

Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case, Wieczór, Miłosz, Genna Vito, Aranda Juan, Badia Rosa M., Gelpí Josep Lluis, Gapsys Vytautas, de Groot Bert L., Lindahl Erik, Municoy Martí, Hospital Adam, et al. , WIREs Computational Molecular Science, 05/2022, Volume In Press, p.e1622, (2022)

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update, López-Ferrando, Víctor, Gazzo Andrea, de la Cruz Xavier, Orozco Modesto, and Gelpí Josep-Lluis , Nucleic Acids Research, 04/2017, Volume 45, Issue W1, p.W222-W228, (2017)

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update, López-Ferrando, Víctor, Gazzo Andrea, de la Cruz Xavier, Orozco Modesto, and Gelpí Josep-Lluis , Nucleic Acids Research, 04/2017, Volume 45, Issue W1, p.W222-W228, (2017)

PMUT: a web-based tool for the annotation of pathological mutations on proteins., Ferrer-Costa, Carles, Gelpí Josep-Lluis, Zamakola Leire, Párraga Iván, de la Cruz Xavier, and Orozco Modesto , Bioinformatics, 2005 Jul 15, Volume 21, p.3176-8, (2005)

pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs, Serrano-Chacón, Israel, Mir Bartomeu, Cupellini Lorenzo, Colizzi Francesco, Orozco Modesto, Escaja Núria, and González Carlos , Journal of the American Chemical Society, 02/2023, Volume 145, Issue 6, p.3696 - 3705, (2023)

Partition of protein solvation into group contributions from molecular dynamics simulations., Morreale, Antonio, de la Cruz Xavier, Meyer Tim, Gelpí Josep-Lluis, F Luque Javier, and Orozco Modesto , Proteins, 2005 Jan 1, Volume 58, p.101-9, (2005)

Parmbsc1: a refined force field for DNA simulations., Ivani, Ivan, Dans Pablo D., Noy Agnes, Pérez Alberto, Faustino Ignacio, Hospital Adam, Walther Jurgen, Andrio Pau, Goni Ramon, Balaceanu Alexandra, et al. , Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)

Parmbsc1: a refined force field for DNA simulations., Ivani, Ivan, Dans Pablo D., Noy Agnes, Pérez Alberto, Faustino Ignacio, Hospital Adam, Walther Jurgen, Andrio Pau, Goni Ramon, Balaceanu Alexandra, et al. , Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)

Parmbsc1: a refined force field for DNA simulations., Ivani, Ivan, Dans Pablo D., Noy Agnes, Pérez Alberto, Faustino Ignacio, Hospital Adam, Walther Jurgen, Andrio Pau, Goni Ramon, Balaceanu Alexandra, et al. , Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems., Emperador, Agustí, Sfriso Pedro, Villarreal Marcos Ariel, Gelpí Josep-Lluis, and Orozco Modesto , J Chem Theory Comput, 2015 Dec 8, Volume 11, p.5929-38, (2015)

The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry, Terrazas, Montserrat, Genna Vito, Portella Guillem, Villegas Núria, Sanchez Dani, Arnan Carme, Pulido-Quetglas Carlos, Johnson Rory, Guigó Roderic, Brun-Heath Isabelle, et al. , Chem, 04/2019, (2019)

The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry, Terrazas, Montserrat, Genna Vito, Portella Guillem, Villegas Núria, Sanchez Dani, Arnan Carme, Pulido-Quetglas Carlos, Johnson Rory, Guigó Roderic, Brun-Heath Isabelle, et al. , Chem, 04/2019, (2019)