Wilma K. Olson

Department of Chemistry & Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers - The State University of New Jersey

Affiliated withRutgers - The State University of New Jersey

Research Area

Biology

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 63	2013

Other Publications

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