Biblio

Found 334 results
[ Author(Desc)] Title Year
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H
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)
Molecular dynamics simulations: advances and applications., Hospital, Adam, J Goñi Ramon, Orozco Modesto, and Gelpí Josep-Lluis , Adv Appl Bioinform Chem, 2015, Volume 8, p.37-47, (2015)
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations., Hospital, Adam, Andrio Pau, Fenollosa Carles, Cicin-Sain Damjan, Orozco Modesto, and Gelpí Josep-Lluis , Bioinformatics, 2012 May 1, Volume 28, p.1278-9, (2012)
The Multiple Roles of Waters in Protein Solvation, Hospital, Adam, Candotti Michela, Gelpí Josep-Lluis, and Orozco Modesto , The Journal of Physical Chemistry B, 01/2017, Issue Klaus Schulten Memorial Issue, (2017)
Surviving the deluge of biosimulation data, Hospital, Adam, Battistini Federica, Soliva Robert, Gelpí Josep Lluis, and Orozco Modesto , Wiley Interdisciplinary Reviews: WIREs Comput Mol Sci, 11/2019, Volume n/a, Issue n/a, p.e1449, (2019)
High-throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure, Hospital, Adam, and Gelpí Josep-Lluis , Wiley Interdisciplinary Reviews: Computational Molecular Science, Volume 3, p.364–377, (2013)
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)
Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives., Huertas, Oscar, Poater Jordi, Fuentes-Cabrera Miguel, Orozco Modesto, Solà Miquel, and F Luque Javier , J Phys Chem A, 2006 Nov 9, Volume 110, p.12249-58, (2006)
J
Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer, Jaeger, Samira, Igea Ana, Arroyo Rodrigo, Alcalde Victor, Canovas Begoña, Orozco Modesto, Nebreda Angel R., and Aloy Patrick , Cancer Research, 01/2017, Volume 77, Issue 2, p.459, (2017)
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)
Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program, Janin, Maxime, Ortiz-Barahona Vanessa, de Moura Manuel Castro, Martinez-Cardus Anna, Llinàs-Arias Pere, Soler Marta, Nachmani Daphna, Pelletier Joffrey, Schumann Ulrike, Calleja-Cervantes Maria E., et al. , Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)
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)
A genome-wide association study identifies SLC8A3 as a susceptibility locus for ACPA-positive rheumatoid arthritis., Julià, Antonio, González Isidoro, Fernández-Nebro Antonio, Blanco Francisco, Rodriguez Luis, González Antonio, Cañete Juan D., Maymó Joan, Alperi-López Mercedes, Olivé Alejandro, et al. , Rheumatology (Oxford), 2016 Jun, Volume 55, p.1106-11, (2016)
A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis., Julià, Antonio, Domènech Eugeni, Chaparro María, García-Sánchez Valle, Gomollón Fernando, Panés Julián, Mañosa Míriam, de Acosta Manuel Barreiro-, Gutiérrez Ana, Garcia-Planella Esther, et al. , Hum Mol Genet, 2014 Dec 20, Volume 23, p.6927-34, (2014)
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 genome-wide association study on a southern European population identifies a new Crohn’s disease susceptibility locus at RBX1-EP300., Julià, Antonio, Domènech Eugeni, Ricart Elena, Tortosa Raül, García-Sánchez Valle, Gisbert Javier P., Mateu Pilar Nos, Gutiérrez Ana, Gomollón Fernando, Mendoza Juan Luís, et al. , Gut, 2013 Oct, Volume 62, p.1440-5, (2013)
K
Theoretical study of the mechanisms of substrate recognition by catalase., Kalko, S G., Gelpí Josep-Lluis, Fita I, and Orozco Modesto , J Am Chem Soc, 2001 Oct 3, Volume 123, p.9665-72, (2001)
On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling"., Klamt, Andreas, Mennucci Benedetta, Tomasi Jacopo, Barone Vincenzo, Curutchet Carles, Orozco Modesto, and F Luque Javier , Acc Chem Res, 2009 Apr 21, Volume 42, p.489-92; discussion 493-7, (2009)
Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs, Kotev, Martin, Manuel-Manresa Pilar, Hernando Elsa, Soto-Cerrato Vanessa, Orozco Modesto, Quesada Roberto, Pérez-Tomás Ricardo, and Guallar Victor , Journal of Chemical Information and Modeling, 08/2017, (2017)
Molecular basis of substrate-induced permeation by an amino acid antiporter., Kowalczyk, Lukasz, Ratera Mercè, Paladino Antonella, Bartoccioni Paola, Errasti-Murugarren Ekaitz, Valencia Eva, Portella Guillem, Bial Susanna, Zorzano Antonio, Fita Ignacio, et al. , Proc Natl Acad Sci U S A, 2011 Mar 8, Volume 108, p.3935-40, (2011)
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia., Kulis, Marta, Heath Simon, Bibikova Marina, Queirós Ana C., Navarro Alba, Clot Guillem, Martínez-Trillos Alejandra, Castellano Giancarlo, Brun-Heath Isabelle, Pinyol Magda, et al. , Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)
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)
An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations, Kuzmanic, Antonija, Dans Pablo D., and Orozco Modesto , Chem, 03/2019, Volume 5, Issue 3, p.649 - 663, (2019)
L
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)
Nucleic acid simulations themed issue., Laughton, Charles A., and Orozco Modesto , Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10541-2, (2009)
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)
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)
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)
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)
M
A hybrid all-atom/coarse grain model for multiscale simulations of DNA, Machado, Matías Rodrigo, Dans Pablo Daniel, and Pantano Sergio , Physical Chemistry Chemical Physics, Volume 13, Number 40, p.18134–18144, (2011)
Isoform-specific determinants in the HP1 binding to histone 3: insights from molecular simulations, Machado, Matias R., Dans Pablo Daniel, and Pantano Sergio , Amino acids, Volume 38, Number 5, p.1571–1581, (2010)
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)
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)
Exploring the binding mode of semicarbazide-sensitive amine oxidase/VAP-1: identification of novel substrates with insulin-like activity., Marti, Luc, Abella Anna, de la Cruz Xavier, García-Vicente Silvia, Unzeta Mercedes, Carpéné Christian, Palacín Manuel, Testar Xavier, Orozco Modesto, and Zorzano Antonio , J Med Chem, 2004 Sep 23, Volume 47, p.4865-74, (2004)
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)
Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation, Martin, Benjamin, Dans Pablo D., Wieczór Milosz, Villegas Núria, Brun-Heath Isabelle, Battistini Federica, Terrazas Montserrat, and Orozco Modesto , PLoS computational biology, 01/2022, Volume 18, Issue 1, p.e1009749 - e1009749, (2022)
Dramatic effect of furanose C2’ substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom., Martín-Pintado, Nerea, Yahyaee-Anzahaee Maryam, Deleavey Glen F., Portella Guillem, Orozco Modesto, Damha Masad J., and González Carlos , J Am Chem Soc, 2013 Apr 10, Volume 135, p.5344-7, (2013)
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)
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)
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)
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)
α1,4-N-Acetylhexosaminyltransferase EXTL2: The Missing Link for Understanding Glycosidic Bond Biosynthesis with Retention of Configuration, Mendoza, Fernanda, Gómez Hansel, Lluch José M., and Masgrau Laura , ACS Catalysis, 2016/04/01, Volume 6, Issue 4, p.2577 - 2589, (2016)
Essential Dynamics: A Tool for Efficient Trajectory Compression and Management, Meyer, Tim, Ferrer-Costa Carles, Pérez Alberto, Rueda Manuel, Bidon-Chanal Axel, F. Luque Javier, Laughton Charles. A., and Orozco Modesto , Journal of Chemical Theory and Computation, 2006/03/01, Volume 2, Issue 2, p.251 - 258, (2006)
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories., Meyer, Tim, D’Abramo Marco, Hospital Adam, Rueda Manuel, Ferrer-Costa Carles, Pérez Alberto, Carrillo Oliver, Camps Jordi, Fenollosa Carles, Repchevsky Dmitry, et al. , Structure, 2010 Nov 10, Volume 18, p.1399-409, (2010)
Proteins in the gas phase, Meyer, Tim, Gabelica Valérie, Grubmüller Helmut, and Orozco Modesto , WIREs Computational Molecular Science, Volume 3, p.408-425, (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)

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