Department of Chemistry & Chemical Biology and BioMaPS Institute for Quantitative Biology
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Interplay of protein and DNA structure revealed in simulations of the lac operon.
PloS one , 2013 | Pubmed ID: 23457581
Bending of DNA by asymmetric charge neutralization: all-atom energy simulations.
Journal of the American Chemical Society May, 2002 | Pubmed ID: 11971734
Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level.
Biophysical journal Jul, 2002 | Pubmed ID: 12080098
Accurate representation of B-DNA double helical structure with implicit solvent and counterions.
Biophysical journal Jul, 2002 | Pubmed ID: 12080128
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.
Nucleic acids research Sep, 2003 | Pubmed ID: 12930962
Implications of the dependence of the elastic properties of DNA on nucleotide sequence.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Jul, 2004 | Pubmed ID: 15306458
Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids.
Biophysical journal Feb, 2005 | Pubmed ID: 15501936
Target-site preferences of Sleeping Beauty transposons.
Journal of molecular biology Feb, 2005 | Pubmed ID: 15663935
Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation.
Proceedings of the National Academy of Sciences of the United States of America Jun, 2006 | Pubmed ID: 16785444
A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning.
Journal of molecular biology Aug, 2007 | Pubmed ID: 17585938
Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor.
Journal of chemical information and modeling Nov-Dec, 2007 | Pubmed ID: 17967005
nuScore: a web-interface for nucleosome positioning predictions.
Bioinformatics (Oxford, England) Jun, 2008 | Pubmed ID: 18445607
Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations.
Journal of molecular biology Oct, 2008 | Pubmed ID: 18586040
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.
Nature protocols , 2008 | Pubmed ID: 18600227
Structure, dynamics, and branch migration of a DNA Holliday junction: a single-molecule fluorescence and modeling study.
Biophysical journal Nov, 2008 | Pubmed ID: 18658216
BPS: a database of RNA base-pair structures.
Nucleic acids research Jan, 2009 | Pubmed ID: 18845572
PREDICTED EFFECTS OF LOCAL CONFORMATIONAL COUPLING AND EXTERNAL RESTRAINTS ON THE TORSIONAL PROPERTIES OF SINGLE DNA MOLECULES.
Multiscale modeling & simulation : a SIAM interdisciplinary journal , 2006 | Pubmed ID: 19081755
New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures.
Methods (San Diego, Calif.) Mar, 2009 | Pubmed ID: 19150407
DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences.
Biophysical journal Mar, 2009 | Pubmed ID: 19289051
Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.
Nucleic acids research Jul, 2009 | Pubmed ID: 19474339
3DNALandscapes: a database for exploring the conformational features of DNA.
Nucleic acids research Jan, 2010 | Pubmed ID: 19906722
Two perspectives on the twist of DNA.
The Journal of chemical physics Dec, 2009 | Pubmed ID: 20059113
How stiff is DNA?
Physical chemistry chemical physics : PCCP Feb, 2010 | Pubmed ID: 20119618
The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.
Nucleic acids research Aug, 2010 | Pubmed ID: 20223772
DNA architecture, deformability, and nucleosome positioning.
Journal of biomolecular structure & dynamics Jun, 2010 | Pubmed ID: 20232929
Long-range effects of histone point mutations on DNA remodeling revealed from computational analyses of SIN-mutant nucleosome structures.
Nucleic acids research Nov, 2010 | Pubmed ID: 20647418
Properties of the Nucleic-acid Bases in Free and Watson-Crick Hydrogen-bonded States: Computational Insights into the Sequence-dependent Features of Double-helical DNA.
Biophysical reviews Mar, 2009 | Pubmed ID: 21218180
Nucleic-acid structural deformability deduced from anisotropic displacement parameters.
Biopolymers Apr, 2011 | Pubmed ID: 21280021
Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins.
Journal of molecular biology Jun, 2011 | Pubmed ID: 21459097
Working the kinks out of nucleosomal DNA.
Current opinion in structural biology Jun, 2011 | Pubmed ID: 21482100
Internucleosomal interactions mediated by histone tails allow distant communication in chromatin.
The Journal of biological chemistry Jun, 2012 | Pubmed ID: 22518845
Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform.
Journal of chemical theory and computation Jan, 2012 | Pubmed ID: 22712001
Computational opportunities for remote collaboration and capacity building afforded by Web 2.0 and cloud computing.
Biophysical reviews Sep, 2012 | Pubmed ID: 23066431
Insights into Gene Expression and Packaging from Computer Simulations.
Biophysical reviews Sep, 2012 | Pubmed ID: 23139731
Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations.
Biochemical Society transactions Apr, 2013 | Pubmed ID: 23514154
Can nucleosomal DNA be described by an elastic model?: Comment on "Sequence-dependent collective properties of DNAs and their role in biological systems" by Pasquale De Santis and Anita Scipioni.
Physics of life reviews Mar, 2013 | Pubmed ID: 23587120
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