Found 31 results
Author Title [ Year(Asc)]
Filters: Keyword is Molecular Dynamics Simulation and Author is Modesto Orozco  [Clear All Filters]
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)
Exploration of conformational transition pathways from coarse-grained simulations., Sfriso, Pedro, Hospital Adam, Emperador Agustí, and Orozco Modesto , Bioinformatics, 2013 Aug 15, Volume 29, p.1980-6, (2013)
Functionalization of the 3’-ends of DNA and RNA strands with N-ethyl-N-coupled nucleosides: a promising approach to avoid 3’-exonuclease-catalyzed hydrolysis of therapeutic oligonucleotides., Terrazas, Montserrat, Alagia Adele, Faustino Ignacio, Orozco Modesto, and Eritja Ramon , Chembiochem, 2013 Mar 4, Volume 14, p.510-20, (2013)
Improved nucleic acid descriptors for siRNA efficacy prediction., Sciabola, Simone, Cao Qing, Orozco Modesto, Faustino Ignacio, and Stanton Robert V. , Nucleic Acids Res, 2013 Feb 1, Volume 41, p.1383-94, (2013)
Light on the structural communication in Ras GTPases., Raimondi, Francesco, Felline Angelo, Portella Guillem, Orozco Modesto, and Fanelli Francesca , J Biomol Struct Dyn, 2013, Volume 31, p.142-57, (2013)
NAFlex: a web server for the study of nucleic acid flexibility., Hospital, Adam, Faustino Ignacio, Collepardo-Guevara Rosana, González Carlos, Gelpí Josep-Lluis, and Orozco Modesto , Nucleic Acids Res, 2013 Jul, Volume 41, p.W47-55, (2013)
Toward an atomistic description of the urea-denatured state of proteins., Candotti, Michela, Esteban-Martín Santiago, Salvatella Xavier, and Orozco Modesto , Proc Natl Acad Sci U S A, 2013 Apr 9, Volume 110, p.5933-8, (2013)
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings., Orozco, Modesto, Orellana Laura, Hospital Adam, Naganathan Athi N., Emperador Agustí, Carrillo Oliver, and Gelpí J L. , Adv Protein Chem Struct Biol, 2011, Volume 85, p.183-215, (2011)
The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding., Naganathan, Athi N., and Orozco Modesto , J Am Chem Soc, 2011 Aug 10, Volume 133, p.12154-61, (2011)
Nucleotide binding switches the information flow in ras GTPases., Raimondi, Francesco, Portella Guillem, Orozco Modesto, and Fanelli Francesca , PLoS Comput Biol, 2011 Mar, Volume 7, p.e1001098, (2011)
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)
Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases., Blas, José Ramón, Huertas Oscar, Tabares Carolina, Sumpter Bobby G., Fuentes-Cabrera Miguel, Orozco Modesto, Ordejón Pablo, and F Luque Javier , J Phys Chem A, 2011 Oct 20, Volume 115, p.11344-54, (2011)
A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks., Stein, Amelie, Rueda Manuel, Panjkovich Alejandro, Orozco Modesto, and Aloy Patrick , Structure, 2011 Jun 8, Volume 19, p.881-9, (2011)
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)
Multiple routes to characterize the folding of a small DNA hairpin., Portella, Guillem, and Orozco Modesto , Angew Chem Int Ed Engl, 2010 Oct 11, Volume 49, p.7673-6, (2010)
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials., Emperador, Agustí, Meyer Tim, and Orozco Modesto , Proteins, 2010 Jan, Volume 78, p.83-94, (2010)
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)
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)
Toward a consensus view of duplex RNA flexibility., Faustino, Ignacio, Pérez Alberto, and Orozco Modesto , Biophys J, 2010 Sep 22, Volume 99, p.1876-85, (2010)