Biblio
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)
Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design,
, Journal of Chemical Theory and Computation, 2012/00/10, Volume 8, p.2204 - 2214, (2012)
Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations,
, Physical Review E, Volume 86, Number 2, p.021903, (2012)
Characterization of the impact of alternative splicing on protein dynamics: the cases of glutathione S-transferase and ectodysplasin-A isoforms.,
, Proteins, 2012 Aug, Volume 80, p.2235-49, (2012)
Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field,
, Journal of Chemical Theory and Computation, 2013/01/08, Volume 9, Issue 1, p.119 - 125, (2012)
Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case.,
, PLoS Comput Biol, 2012, Volume 8, p.e1002647, (2012)
Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels.,
, Biophys J, 2012 Oct 17, Volume 103, p.1698-705, (2012)
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.,
, Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)
Essential role of glutamate 317 in galactosyl transfer by α3GalT: a computational study.,
, Carbohydr Res, 2012 Jul 15, Volume 356, p.204-8, (2012)
Evidence for transcript networks composed of chimeric RNAs in human cells.,
, PLoS One, 2012, Volume 7, p.e28213, (2012)
Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia.,
, Nat Genet, 2012 Jan, Volume 44, p.47-52, (2012)
Exploring polymorphisms in B-DNA helical conformations.,
, Nucleic Acids Res, 2012 Nov, Volume 40, p.10668-78, (2012)
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations,
, Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012)
Frontiers in molecular dynamics simulations of DNA.,
, Acc Chem Res, 2012 Feb 21, Volume 45, p.196-205, (2012)
Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling.,
, Genome Biol, 2012, Volume 13, p.R106, (2012)
htSeqTools: high-throughput sequencing quality control, processing and visualization in R.,
, Bioinformatics, 2012 Feb 15, Volume 28, p.589-90, (2012)
Impact of methylation on the physical properties of DNA.,
, Biophys J, 2012 May 2, Volume 102, p.2140-8, (2012)
Ligand-induced formation of transient dimers of mammalian 12/15-lipoxygenase: a key to allosteric behavior of this class of enzymes?,
, Proteins, 2012 Mar, Volume 80, p.703-12, (2012)
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.,
, Bioinformatics, 2012 May 1, Volume 28, p.1278-9, (2012)
Retaining glycosyltransferase mechanism studied by QM/MM methods: lipopolysaccharyl-α-1,4-galactosyltransferase C transfers α-galactose via an oxocarbenium ion-like transition state.,
, J Am Chem Soc, 2012 Mar 14, Volume 134, p.4743-52, (2012)
Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes.,
, Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)
Structure of triplex DNA in the gas phase.,
, J Am Chem Soc, 2012 Apr 18, Volume 134, p.6596-606, (2012)
Structure-based identification of new high-affinity nucleosome binding sequences.,
, J Mol Biol, 2012 Jun 29, Volume 420, p.8-16, (2012)
The tomato genome sequence provides insights into fleshy fruit evolution.,
, Nature, 2012 May 31, Volume 485, p.635-41, (2012)
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)
Assessing the Accuracy of the SIRAH Force Field to Model DNA at Coarse Grain Level,
, Advances in Bioinformatics and Computational Biology, p.71–81, (2013)
Backbone FC-H···O hydrogen bonds in 2’F-substituted nucleic acids.,
, Angew Chem Int Ed Engl, 2013 Nov 11, Volume 52, p.12065-8, (2013)
The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors.,
, FASEB J, 2013 Mar, Volume 27, p.1048-61, (2013)
Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.,
, Nucleic Acids Res, 2013 Feb 1, Volume 41, p.2723-35, (2013)
The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator.,
, The Journal of Physical Chemistry B, 2013/00/15, (2013)
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)
The dynamic view of proteins: comment on "Comparing proteins to their internal dynamics: exploring structure-function relationships beyond static structural alignments".,
, Phys Life Rev, 2013 Mar, Volume 10, p.29-30; discussion 39-40, (2013)
Effect of zinc and calcium ions on the rat kidney membrane-bound form of dipeptidyl peptidase IV.,
, J Biosci, 2013 Sep, Volume 38, p.461-9, (2013)
Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations,
, Journal of Chemical Theory and Computation, Volume 9, p.1222-1229, (2013)
Enzyme-directed mutasynthesis: a combined experimental and theoretical approach to substrate recognition of a polyketide synthase.,
, ACS Chem Biol, 2013 Feb 15, Volume 8, p.443-50, (2013)