Biblio
Unveiling case-control relationships in designing a simple and powerful method for detecting gene-gene interactions.,
, Genet Epidemiol, 2012 Nov, Volume 36, p.710-6, (2012)
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.,
, 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.,
, Int J Biochem Cell Biol, 2011 Mar, Volume 43, p.363-71, (2011)
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)
A hybrid all-atom/coarse grain model for multiscale simulations of DNA,
, Physical Chemistry Chemical Physics, Volume 13, Number 40, p.18134–18144, (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)
Nucleotide binding switches the information flow in ras GTPases.,
, PLoS Comput Biol, 2011 Mar, Volume 7, p.e1001098, (2011)
nucleR: a package for non-parametric nucleosome positioning.,
, Bioinformatics, 2011 Aug 1, Volume 27, p.2149-50, (2011)
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast.,
, BMC Genomics, 2011, Volume 12, p.489, (2011)
Polarization effects in molecular interactions,
, WIREs Comput Mol Sci, 2011, Volume 1, p.844 - 854, (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)
Switching reversibility to irreversibility in glycogen synthase kinase 3 inhibitors: clues for specific design of new compounds,
, Journal of medicinal chemistry, Volume 54, Number 12, p.4042–4056, (2011)
A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks.,
, Structure, 2011 Jun 8, Volume 19, p.881-9, (2011)
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.,
, Nature, 2011 Jul 7, Volume 475, p.101-5, (2011)
Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?,
, Journal of Chemical Theory and Computation, Volume 6, Number 12, p.3793–3807, (2010)
Approaching Elastic Network Models to Molecular Dynamics Flexibility,
, Journal of Chemical Theory and Computation, Volume 6, p.2910-2923, (2010)
A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics,
, 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.,
, 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)
The EMBRACE web service collection,
, Nucleic Acids Research, Volume 38, p.W683-W688, (2010)
Enabling HMMER for the Grid with COMP Superscalar,
, Procedia Computer Science, Volume 1, p.2629–2638, (2010)
A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins.,
, 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,
, Amino acids, Volume 38, Number 5, p.1571–1581, (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)
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.,
, Proteins, 2010 Jan, Volume 78, p.83-94, (2010)
Real-time atomistic description of DNA unfolding.,
, 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.,
, J Mol Biol, 2010 Oct 22, Volume 403, p.217-30, (2010)
Structural mechanics of DNA wrapping in the nucleosome.,
, J Mol Biol, 2010 Feb 19, Volume 396, p.264-79, (2010)
Structural properties of g,t-parallel duplexes.,
, 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,
, 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.,
, 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.,
, J Am Chem Soc, 2010 May 5, Volume 132, p.5993-6000, (2010)
Toward a consensus view of duplex RNA flexibility.,
, 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.,
, 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.,
, Comp Funct Genomics, 2009, p.905894, (2009)
An atomistic view to the gas phase proteome.,
, Structure, 2009 Jan 14, Volume 17, p.88-95, (2009)
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)
Density functional theory characterization and descriptive analysis of cisplatin and related compounds,
, Journal of chemical information and modeling, Volume 49, Number 6, p.1407–1419, (2009)
FlexServ: an integrated tool for the analysis of protein flexibility.,
, Bioinformatics, 2009 Jul 1, Volume 25, p.1709-10, (2009)
The impact of monovalent ion force field model in nucleic acids simulations.,
, Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10596-607, (2009)
Nucleic acid simulations themed issue.,
, 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".,
, Acc Chem Res, 2009 Apr 21, Volume 42, p.489-92; discussion 493-7, (2009)