VDNA: the virtual DNA plug-in for VMD.
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.


BACKGROUND
VDNA is pre-installed in VMD, http://www.ks.uiuc.edu/Research/vmd. Updates are at http://dna.ccs.tulane.edu.
Bishop
Thomas C
TC
Center for Computational Science, Tulane University, Lindy Boggs Center Suite 500, New Orleans, LA 70118, USA. bishop@tulane.edu
D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012984:Software; D013329:Structure-Activity Relationship
D004247:DNA