Biblio

Found 164 results
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M
Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins, Barbany, Montserrat, Meyer Tim, Hospital Adam, Faustino Ignacio, D’Abramo Marco, Morata Jordi, Orozco Modesto, and de la Cruz Xavier , PLoS ONE, 2015/03/27, Volume 10, p.e0119978 -, (2015)
A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level, Walther, Jurgen, Dans Pablo D., Balaceanu Alexandra, Hospital Adam, Bayarri Genis, and Orozco Modesto , Nucleic Acids Research, 01/2020, (2020)
Multiscale simulation of DNA, Dans, Pablo D., Walther Jurgen, Gómez Hansel, and Orozco Modesto , Current Opinions in Structural Biology - Theory and simulation • Macromolecular machines 2016, 02/2016, Volume 37, p.29 - 45, (2016)
Mutation in KARS: A novel mechanism for severe anaphylaxis, Ribó, Pau, Guo Yanru, Aranda Juan, Ainsua-Enrich Erola, Navinés-Ferrer Arnau, Guerrero Mario, Pascal Mariona, de la Cruz Cinthia, Orozco Modesto, Muñoz-Cano Rosa, et al. , Journal of Allergy and Clinical Immunology, 05/2021, Volume 147, Issue 5, p.1855 - 1864.e9, (2021)
Mutations in JMJD1C are involved in Rett syndrome and intellectual disability., Sáez, Mauricio A., Fernández-Rodríguez Juana, Moutinho Catia, Sanchez-Mut Jose V., Gomez Antonio, Vidal Enrique, Petazzi Paolo, Szczesna Karolina, Lopez-Serra Paula, Lucariello Mario, et al. , Genet Med, 2016 Apr, Volume 18, Issue 4, p.378-85, (2016)
Mutations in JMJD1C are involved in Rett syndrome and intellectual disability., Sáez, Mauricio A., Fernández-Rodríguez Juana, Moutinho Catia, Sanchez-Mut Jose V., Gomez Antonio, Vidal Enrique, Petazzi Paolo, Szczesna Karolina, Lopez-Serra Paula, Lucariello Mario, et al. , Genet Med, 2016 Apr, Volume 18, Issue 4, p.378-85, (2016)
P
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)
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)
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast., Deniz, Ozgen, Flores Oscar, Battistini Federica, Pérez Alberto, Soler-López Montserrat, and Orozco Modesto , BMC Genomics, 2011, Volume 12, p.489, (2011)
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)
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)
Polarization effects in molecular interactions, F Luque, Javier, Dehez François, Chipot Christophe, and Orozco Modesto , WIREs Comput Mol Sci, 2011, Volume 1, p.844 - 854, (2011)
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)
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)
A procedure for identifying homologous alternative splicing events., Talavera, David, Hospital Adam, Orozco Modesto, and de la Cruz Xavier , BMC Bioinformatics, 2007, Volume 8, p.260, (2007)
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)
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes., Conde, Lucía, Vaquerizas Juan M., Ferrer-Costa Carles, de la Cruz Xavier, Orozco Modesto, and Dopazo Joaquin , Nucleic Acids Res, 2005 Jul 1, Volume 33, p.W501-5, (2005)
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes., Conde, Lucía, Vaquerizas Juan M., Ferrer-Costa Carles, de la Cruz Xavier, Orozco Modesto, and Dopazo Joaquin , Nucleic Acids Res, 2005 Jul 1, Volume 33, p.W501-5, (2005)
R
Repair of UV-Induced DNA Damage Independent of Nucleotide Excision Repair Is Masked by MUTYH, Mazouzi, Abdelghani, Battistini Federica, Moser Sarah C., da Silva Joana Ferreira, Wiedner Marc, Owusu Michel, Lardeau Charles-Hugues, Ringler Anna, Weil Beatrix, Neesen Jürgen, et al. , Molecular Cell, 11/2017, Volume 68, Issue 4, p.797 - 807, (2017)
Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins, Sfriso, Pedro, Duran-Frigola Miquel, Mosca Roberto, Emperador Agustí, Aloy Patrick, and Orozco Modesto , Structure, Volume 24, p.116 - 126, (2016)
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)
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)
The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA, Balaceanu, Alexandra, Pasi Marco, Dans Pablo D., Hospital Adam, Lavery Richard, and Orozco Modesto , The Journal of Physical Chemistry Letters, 01/01/2017, Volume 8, p.21 - 28, (2017)
S
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)
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking., Pons, Carles, Talavera David, de la Cruz Xavier, Orozco Modesto, and Fernandez-Recio Juan , J Chem Inf Model, 2011 Feb 28, Volume 51, p.370-7, (2011)
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)
Seven-Membered Ring Nucleoside Analogues: Stereoselective Synthesis and Studies on Their Conformational Properties, Habibian, Maryam, Martínez-Montero Saúl, Portella Guillem, Chua Zhijie, D. Bohle Scott, Orozco Modesto, and Damha Masad J. , Organic Letters, 11/2015, Volume 17, Issue 21, p.5416 - 5419, (2015)
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)
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)
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)
The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules, Dans, Pablo D., Balaceanu Alexandra, Pasi Marco, Patelli Alessandro S., Petkevičiūtė Daiva, Walther Jurgen, Hospital Adam, Bayarri Genis, Lavery Richard, Maddocks John H., et al. , Nucleic Acids Research, 10/2019, (2019)
Structural and Energetic Study of Cisplatin and Derivatives: Comparison of the Performance of Density Funtional Theory Implementations, Dans, Pablo Daniel, Crespo Alejandro, Estrin Darío A., and E Coitiño Laura , Journal of Chemical Theory and Computation, Volume 4, Number 5, p.740–750, (2008)
Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data., Pons, Carles, D’Abramo Marco, Svergun Dmitri I., Orozco Modesto, Bernadó Pau, and Fernandez-Recio Juan , J Mol Biol, 2010 Oct 22, Volume 403, p.217-30, (2010)
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)
Structure and Dynamics of Oligonucleotides in the Gas Phase, Arcella, Annalisa, Dreyer Jens, Ippoliti Emiliano, Ivani Ivan, Portella Guillem, Gabelica Valérie, Carloni Paolo, and Orozco Modesto , Angewandte Chemie International Edition, 01/2015, Volume 54, p.467–471, (2015)
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane., Fort, Joana, de la Ballina Laura R., Burghardt Hans E., Ferrer-Costa Carles, Turnay Javier, Ferrer-Orta Cristina, Usón Isabel, Zorzano Antonio, Fernandez-Recio Juan, Orozco Modesto, et al. , J Biol Chem, 2007 Oct 26, Volume 282, p.31444-52, (2007)
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer., Dršata, Tomáš, Pérez Alberto, Orozco Modesto, Morozov Alexandre V., Sponer Jiřĺ, and Lankaš Filip , J Chem Theory Comput, 2013, Volume 9, p.707-721, (2013)
Subcellular localization of the interaction between the human immunodeficiency virus transactivator Tat and the nucleosome assembly protein 1, De Marco, Alex, Dans Pablo Daniel, Knezevich Anna, Maiuri Paolo, Pantano Sergio, and Marcello Alessandro , Amino acids, Volume 38, Number 5, p.1583–1593, (2010)
Subcellular localization of the interaction between the human immunodeficiency virus transactivator Tat and the nucleosome assembly protein 1, De Marco, Alex, Dans Pablo Daniel, Knezevich Anna, Maiuri Paolo, Pantano Sergio, and Marcello Alessandro , Amino acids, Volume 38, Number 5, p.1583–1593, (2010)
Switching reversibility to irreversibility in glycogen synthase kinase 3 inhibitors: clues for specific design of new compounds, Perez, Daniel I., Palomo Valle, Pérez Concepción, Gil Carmen, Dans Pablo Daniel, F Luque Javier, Conde Santiago, and Martínez Ana , Journal of medicinal chemistry, Volume 54, Number 12, p.4042–4056, (2011)
Synthesis and Properties of 2'-Deoxy-2',4'-difluoroarabinose-Modified Nucleic Acids, Martínez-Montero, Saúl, Deleavey Glen F., Dierker-Viik Arden, Lindovska Petra, Ilina Tatiana, Portella Guillem, Orozco Modesto, Parniak Michael A., González Carlos, and Damha Masad J. , The Journal of Organic Chemistry, 2015/03/20, Volume 80, Issue 6, p.3083 - 3091, (2015)
Synthesis and Properties of 2'-Deoxy-2',4'-difluoroarabinose-Modified Nucleic Acids, Martínez-Montero, Saúl, Deleavey Glen F., Dierker-Viik Arden, Lindovska Petra, Ilina Tatiana, Portella Guillem, Orozco Modesto, Parniak Michael A., González Carlos, and Damha Masad J. , The Journal of Organic Chemistry, 2015/03/20, Volume 80, Issue 6, p.3083 - 3091, (2015)
Synthesis and Properties of 2'-Deoxy-2',4'-difluoroarabinose-Modified Nucleic Acids, Martínez-Montero, Saúl, Deleavey Glen F., Dierker-Viik Arden, Lindovska Petra, Ilina Tatiana, Portella Guillem, Orozco Modesto, Parniak Michael A., González Carlos, and Damha Masad J. , The Journal of Organic Chemistry, 2015/03/20, Volume 80, Issue 6, p.3083 - 3091, (2015)
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA., Lavery, Richard, Zakrzewska Krystyna, Beveridge David, Bishop Thomas C., Case David A., Cheatham Thomas, Dixit Surjit, Jayaram B, Lankaš Filip, Laughton Charles, et al. , Nucleic Acids Res, 2010 Jan, Volume 38, p.299-313, (2010)

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