DIAMOD: display and modeling of DNA bending.
BACKGROUND
DIAMOD (Displayandmodeling ofDNA) was created as a user-friendly software for exploring and better understanding DNA structural variations, particularly DNA bending. It was intended to be as open as possible so that any of the existing or future predictive models can be used with it.


RESULTS
DIAMOD features graphic display and interactive manipulation of DNA molecules on the screen. Since it works with di-, tri- or tetranucleotide models supplied as external files of angular parameters, it was recently used to evaluate critically all available predictive models for DNA bending. The program has a unique option to insert bends at defined positions in DNA sequence independently of the currently used model, which enables the simulation of both intrinsic and protein-induced kinking. Finally, many output file formats facilitate the sharing of data with other programs and the creation of visually pleasing images.


BACKGROUND
The program is available on request to academic users free of charge. It will be distributed via the WWW (http://www-personal.umich.edu/ mensur/software.html). Users with no network access can get a copy directly from the author.


BACKGROUND
mensur@umich.edu
Dlakic
M
M
Department of Biochemistry 330, University of Nevada at Reno, Reno, NV 89557-0014, USA. mensur@umich.edu
Harrington
R E
RE
D000465:Algorithms; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry*; D003626:Data Display; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D012091:Repetitive Sequences, Nucleic Acid; D012984:Software
D004247:DNA