Biblio
Found 84 results
Author Title [ Year] Filters: Keyword is Models and Author is Modesto Orozco [Clear All Filters]
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.,
, J Phys Chem B, 2008 Jul 10, Volume 112, p.8188-97, (2008)
GRID-MD-A tool for massive simulation of protein channels.,
, Proteins, 2008 Feb 15, Volume 70, p.892-9, (2008)
Recent advances in the study of nucleic acid flexibility by molecular dynamics.,
, 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.,
, J Org Chem, 2008 Oct 3, Volume 73, p.7756-63, (2008)
Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility.,
, J Am Chem Soc, 2008 Mar 19, Volume 130, p.3486-96, (2008)
Towards a molecular dynamics consensus view of B-DNA flexibility.,
, Nucleic Acids Res, 2008 Apr, Volume 36, p.2379-94, (2008)
COCO: a simple tool to enrich the representation of conformational variability in NMR structures.,
, Proteins, 2009 Apr, Volume 75, p.206-16, (2009)
Comparison of molecular dynamics and superfamily spaces of protein domain deformation.,
, 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.,
, Nucleic Acids Res, 2009 Sep, Volume 37, p.5589-601, (2009)
On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling".,
, 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.,
, J Phys Chem B, 2009 Jul 9, Volume 113, p.9330-4, (2009)
Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution.,
, J Am Chem Soc, 2009 Nov 4, Volume 131, p.15678-86, (2009)
Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily.,
, 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.,
, Nucleic Acids Res, 2010 Apr, Volume 38, p.2498-511, (2010)
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.,
, Structure, 2010 Nov 10, Volume 18, p.1399-409, (2010)
Multiple routes to characterize the folding of a small DNA hairpin.,
, 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.,
, J Comput Aided Mol Des, 2010 Apr, Volume 24, p.281-91, (2010)
Real-time atomistic description of DNA unfolding.,
, Angew Chem Int Ed Engl, 2010 Jun 28, Volume 49, p.4805-8, (2010)
Effects of local electric fields on the redox free energy of single stranded DNA.,
, Chem Commun (Camb), 2011 Mar 7, Volume 47, p.2646-8, (2011)
Molecular basis of substrate-induced permeation by an amino acid antiporter.,
, Proc Natl Acad Sci U S A, 2011 Mar 8, Volume 108, p.3935-40, (2011)
The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding.,
, J Am Chem Soc, 2011 Aug 10, Volume 133, p.12154-61, (2011)
The protein folding transition-state ensemble from a Go-like model.,
, Phys Chem Chem Phys, 2011 Sep 7, Volume 13, p.15166-74, (2011)
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking.,
, J Chem Inf Model, 2011 Feb 28, Volume 51, p.370-7, (2011)
Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering.,
, J Mol Biol, 2011 Mar 4, Volume 406, p.604-19, (2011)
Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases.,
, J Phys Chem A, 2011 Oct 20, Volume 115, p.11344-54, (2011)
Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case.,
, PLoS Comput Biol, 2012, Volume 8, p.e1002647, (2012)
Evidence for transcript networks composed of chimeric RNAs in human cells.,
, PLoS One, 2012, Volume 7, p.e28213, (2012)
Frontiers in molecular dynamics simulations of DNA.,
, Acc Chem Res, 2012 Feb 21, Volume 45, p.196-205, (2012)
Impact of methylation on the physical properties of DNA.,
, Biophys J, 2012 May 2, Volume 102, p.2140-8, (2012)
Dramatic effect of furanose C2’ substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom.,
, J Am Chem Soc, 2013 Apr 10, Volume 135, p.5344-7, (2013)
Improved nucleic acid descriptors for siRNA efficacy prediction.,
, Nucleic Acids Res, 2013 Feb 1, Volume 41, p.1383-94, (2013)
Direct measurement of the dielectric polarization properties of DNA.,
, Proc Natl Acad Sci U S A, 2014 Sep 2, Volume 111, p.E3624-30, (2014)
The structural impact of DNA mismatches.,
, Nucleic Acids Res, 2015 Apr 30, Volume 43, p.4309-21, (2015)
Visualizing phosphodiester-bond hydrolysis by an endonuclease.,
, Nat Struct Mol Biol, 2015 Jan, Volume 22, p.65-72, (2015)