Biblio

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)

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)

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)

Density functional theory characterization and descriptive analysis of cisplatin and related compounds, Dans, Pablo Daniel, and E Coitiño Laura , Journal of chemical information and modeling, Volume 49, Number 6, p.1407–1419, (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)

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)

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)

Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors., Castaño, Tania, Wang Huanchen, Campillo Nuria E., Ballester Sara, González-García Coral, Hernández Javier, Pérez Concepción, Cuenca Jimena, Pérez-Castillo Ana, Martínez Ana, et al. , ChemMedChem, 2009 May, Volume 4, p.866-76, (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)

Thienylhalomethylketones: Irreversible glycogen synthase kinase 3 inhibitors as useful pharmacological tools., Perez, Daniel I., Conde Santiago, Pérez Concepción, Gil Carmen, Simon Diana, Wandosell Francisco, Moreno Francisco J., Gelpí Josep-Lluis, Luque Francisco J., and Martínez Ana , Bioorg Med Chem, 2009 Oct 1, Volume 17, p.6914-25, (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)

Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?, Darré, Leonardo, Machado Matias R., Dans Pablo Daniel, Herrera Fernando E., and Pantano Sergio , Journal of Chemical Theory and Computation, Volume 6, Number 12, p.3793–3807, (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)

A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics, Dans, Pablo Daniel, Zeida Ari, Machado Matías R., and Pantano Sergio , Journal of Chemical Theory and Computation, Volume 6, Number 5, p.1711–1725, (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)

The EMBRACE web service collection, Pettifer, Steve, Ison Jon, Kalaš Matúš, Thorne Dave, McDermott Philip, Jonassen Inge, Liaquat Ali, Fernández José M., Rodriguez Jose M., Partners INB-, et al. , Nucleic Acids Research, Volume 38, p.W683-W688, (2010)

Enabling HMMER for the Grid with COMP Superscalar, Tejedor, Enric, Badia Rosa M., Royo Romina, and Gelpí Josep-Lluis , Procedia Computer Science, Volume 1, p.2629–2638, (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)

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)

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 mechanics of DNA wrapping in the nucleosome., Battistini, Federica, Hunter Christopher A., Gardiner Eleanor J., and Packer Martin J. , J Mol Biol, 2010 Feb 19, Volume 396, p.264-79, (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)

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)

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)

Time averaging of NMR chemical shifts in the MLF peptide in the solid state., De Gortari, Itzam, Portella Guillem, Salvatella Xavier, Bajaj Vikram S., van der Wel Patrick C. A., Yates Jonathan R., Segall Matthew D., Pickard Chris J., Payne Mike C., and Vendruscolo Michele , J Am Chem Soc, 2010 May 5, Volume 132, p.5993-6000, (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)

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)

Effect of divalent cations on the porcine kidney cortex membrane-bound form of dipeptidyl peptidase IV., Pascual, Isel, Gómez Hansel, Pons Tirso, Chappé Mae, Vargas Miguel Angel, Valdés Gilberto, Lopéz Alí, Saroyán Angélika, Charli Jean-Louis, and Chávez María de los Ang , Int J Biochem Cell Biol, 2011 Mar, Volume 43, p.363-71, (2011)