Biblio

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Pinyol Magda, Quesada Víctor, Conde Laura, Ordóñez Gonzalo R., Villamor Neus, Escaramis Georgia, Jares Pedro, Beà Sílvia, González-Díaz Marcos, et al. , Nature, 2011 Jul 7, Volume 475, p.101-5, (2011)

Approaching Elastic Network Models to Molecular Dynamics Flexibility, Orellana, Laura, Rueda Manuel, Ferrer-Costa Carles, Lopez-Blanco José Ramón, Chacón Pablo, and Orozco Modesto , Journal of Chemical Theory and Computation, Volume 6, p.2910-2923, (2010)

Approaching Elastic Network Models to Molecular Dynamics Flexibility, Orellana, Laura, Rueda Manuel, Ferrer-Costa Carles, Lopez-Blanco José Ramón, Chacón Pablo, and Orozco Modesto , Journal of Chemical Theory and Computation, Volume 6, p.2910-2923, (2010)

Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily., Raimondi, Francesco, Orozco Modesto, and Fanelli Francesca , Structure, 2010 Mar 10, Volume 18, p.402-14, (2010)

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)

A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins., Novoa, Eva Maria, de Moura Manuel Castro, Orozco Modesto, and de Pouplana Lluís Ribas , FEBS Lett, 2010 Jan 21, Volume 584, p.460-6, (2010)

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)

Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies., Soteras, Ignacio, Orozco Modesto, and F Luque Javier , J Comput Aided Mol Des, 2010 Apr, Volume 24, p.281-91, (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)

Real-time atomistic description of DNA unfolding., Pérez, Alberto, and Orozco Modesto , Angew Chem Int Ed Engl, 2010 Jun 28, Volume 49, p.4805-8, (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)

Structural properties of g,t-parallel duplexes., Aviñó, Anna, Cubero Elena, Gargallo Raimundo, González Carlos, Orozco Modesto, and Eritja Ramon , J Nucleic Acids, 2010, Volume 2010, (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)

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)

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)

Alternative splicing of transcription factors’ genes: beyond the increase of proteome diversity., Talavera, David, Orozco Modesto, and de la Cruz Xavier , Comp Funct Genomics, 2009, p.905894, (2009)

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)

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)

Comparison of molecular dynamics and superfamily spaces of protein domain deformation., Velázquez-Muriel, Javier A., Rueda Manuel, Cuesta Isabel, Pascual-Montano Alberto, Orozco Modesto, and Carazo José-María , BMC Struct Biol, 2009, Volume 9, p.6, (2009)

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)

FlexServ: an integrated tool for the analysis of protein flexibility., Camps, Jordi, Carrillo Oliver, Emperador Agustí, Orellana Laura, Hospital Adam, Rueda Manuel, Cicin-Sain Damjan, D’Abramo Marco, Gelpí Josep-Lluis, and Orozco Modesto , Bioinformatics, 2009 Jul 1, Volume 25, p.1709-10, (2009)

FlexServ: an integrated tool for the analysis of protein flexibility., Camps, Jordi, Carrillo Oliver, Emperador Agustí, Orellana Laura, Hospital Adam, Rueda Manuel, Cicin-Sain Damjan, D’Abramo Marco, Gelpí Josep-Lluis, and Orozco Modesto , Bioinformatics, 2009 Jul 1, Volume 25, p.1709-10, (2009)

The impact of monovalent ion force field model in nucleic acids simulations., Noy, Agnes, Soteras Ignacio, F Luque Javier, and Orozco Modesto , Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10596-607, (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)

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)

Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies., Soteras, Ignacio, Forti Flavio, Orozco Modesto, and F Luque Javier , J Phys Chem B, 2009 Jul 9, Volume 113, p.9330-4, (2009)

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields, Fadrná, Eva, Špačková Nad’a, Sarzyñska Joanna, Koča Jaroslav, Orozco Modesto, Cheatham Thomas E., Kulinski Tadeusz, and Šponer Jiří , Journal of Chemical Theory and Computation, 2009/09/08, Volume 5, Issue 9, p.2514 - 2530, (2009)

Solvation enthalpies of neutral solutes in water and octanol, Bidon-Chanal, Axel, Huertas Oscar, Orozco Modesto, and F Luque Javier , Theoretical Chemistry Accounts, 2009/05/01, Volume 123, p.11-20, (2009)

Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution., García-Fandiño, Rebeca, Granja Juan R., D’Abramo Marco, and Orozco Modesto , J Am Chem Soc, 2009 Nov 4, Volume 131, p.15678-86, (2009)

Unique tautomeric and recognition properties of thioketothymines?, Faustino, Ignacio, Aviñó Anna, Marchán Ivan, F Luque Javier, Eritja Ramon, and Orozco Modesto , J Am Chem Soc, 2009 Sep 9, Volume 131, p.12845-53, (2009)

The use of conformationally rigid nucleoside probes to study 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 Symp Ser (Oxf), 2009, p.109-10, (2009)

On the Use of low-resolution Data to Improve Structure Prediction of Proteins and Protein Complexes, D’Abramo, Marco, Meyer Tim, Bernadó Pau, Pons Carles, Recio Juan Fernánde, and Orozco Modesto , Journal of Chemical Theory and Computation, 2009/11/10, Volume 5, Issue 11, p.3129 - 3137, (2009)

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water., Xie, Wangshen, Orozco Modesto, Truhlar Donald G., and Gao Jiali , J Chem Theory Comput, 2009 Feb 17, Volume 5, p.459-467, (2009)

8-Amino guanine accelerates tetramolecular G-quadruplex formation., Gros, Julien, Aviñó Anna, de la Osa Jaime Lopez, González Carlos, Lacroix Laurent, Pérez Alberto, Orozco Modesto, Eritja Ramon, and Mergny Jean-Louis , Chem Commun (Camb), 2008 Jul 7, p.2926-8, (2008)

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)

DNAlive: a tool for the physical analysis of DNA at the genomic scale., J Goñi, Ramon, Fenollosa Carlos, Pérez Alberto, Torrents David, and Orozco Modesto , Bioinformatics, 2008 Aug 1, Volume 24, p.1731-2, (2008)

Exploring the suitability of coarse-grained techniques for the representation of protein dynamics., Emperador, Agustí, Carrillo Oliver, Rueda Manuel, and Orozco Modesto , Biophys J, 2008 Sep, Volume 95, p.2127-38, (2008)

Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian., Forti, Flavio, Barril Xavier, F Luque Javier, and Orozco Modesto , J Comput Chem, 2008 Mar, Volume 29, p.578-87, (2008)

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids., Svozil, Daniel, Sponer Judit E., Marchán Ivan, Pérez Alberto, Cheatham Thomas E., Forti F, F Luque Javier, Orozco Modesto, and Sponer Jiri , J Phys Chem B, 2008 Jul 10, Volume 112, p.8188-97, (2008)

GRID-MD-A tool for massive simulation of protein channels., Carrillo, Oliver, and Orozco Modesto , Proteins, 2008 Feb 15, Volume 70, p.892-9, (2008)

Induction effects in metal cation-benzene complexes., Soteras, Ignacio, Orozco Modesto, and F Luque Javier , Phys Chem Chem Phys, 2008 May 21, Volume 10, p.2616-24, (2008)

Interoperability with Moby 1.0–it’s better than sharing your toothbrush!, Wilkinson, Mark D., Senger Martin, Kawas Edward, Bruskiewich Richard, Gouzy Jerome, Noirot Celine, Bardou Philippe, Ng Ambrose, Haase Dirk, Saiz Enrique de Andres, et al. , Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)

Interoperability with Moby 1.0–it’s better than sharing your toothbrush!, Wilkinson, Mark D., Senger Martin, Kawas Edward, Bruskiewich Richard, Gouzy Jerome, Noirot Celine, Bardou Philippe, Ng Ambrose, Haase Dirk, Saiz Enrique de Andres, et al. , Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)

Recent advances in the study of nucleic acid flexibility by molecular dynamics., Orozco, Modesto, Noy Agnes, and Pérez Alberto , Curr Opin Struct Biol, 2008 Apr, Volume 18, p.185-93, (2008)

Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams., Soteras, Ignacio, Lozano Oscar, Escolano Carmen, Orozco Modesto, Amat Mercedes, Bosch Joan, and F Luque Javier , J Org Chem, 2008 Oct 3, Volume 73, p.7756-63, (2008)

Target flexibility: an emerging consideration in drug discovery and design., Cozzini, Pietro, Kellogg Glen E., Spyrakis Francesca, Abraham Donald J., Costantino Gabriele, Emerson Andrew, Fanelli Francesca, Gohlke Holger, Kuhn Leslie A., Morris Garrett M., et al. , J Med Chem, 2008 Oct 23, Volume 51, p.6237-55, (2008)

Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility., Noy, Agnes, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2008 Mar 19, Volume 130, p.3486-96, (2008)

Towards a molecular dynamics consensus view of B-DNA flexibility., Pérez, Alberto, Lankaš Filip, F Luque Javier, and Orozco Modesto , Nucleic Acids Res, 2008 Apr, Volume 36, p.2379-94, (2008)