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Bioinformatics Advance Access published online on September 29, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp566
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

VDNA: The Virtual DNA plug-in for VMD

Thomas C. Bishop *

Tulane University, Center for Computational Sciences, Lindy Boggs Center Suite 500, New Orleans, LA 70118

*To whom correspondence should be addressed. Prof. Thomas Bishop, E-mail: bishop{at}tulane.edu


  Abstract

Summary: The DNA inter base pair step parameters (Tilt, Roll, Twist, Shift, Slide, Rise) are a standard internal coordinate representation of DNA. In the absence of bend and shear, it is relatively easy to mentally visualize how Twist and Rise generate the familiar double helix. More complex structures do not readily yield to such intuition. For this reason we developed a plug-in for VMD that accepts a set of mathematical expressions as input and generates a coarse-grained model of DNA as output. This feature of VDNA appears to provide a unique approach to DNA modeling. Predefined expressions include: linear, sheared, bent, and circular DNA and models of the nucleosome superhelix, chromatin, thermal motion, and nucleosome unwrapping. Availability: VDNA is preinstalled in VMD, http://www.ks.uiuc.edu/Research/vmd. Updates are at http://dna.ccs.tulane.edu. Contact: bishop{at}tulane.edu

Associate Editor: Prof. Anna Tramontano

Received on July 3, 2009; revised on August 18, 2009; accepted on September 10, 2009

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