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Users' contributions / deformation energy calculation program

« on: December 15, 2008, 03:01:29 pm »

Hello,

I have written a program in C to calculate deformation energy scores on DNA duplexes from 3DNA output, based on X-ray averages and force constants at the base-pair or base-pair step level. This program gives not only the total deformation energy but also its components. I attach an archive containing the program as well as 3DNA output files to perform two tests:

deform_energy.tar.gz

- deformation energy of DNA in the 1kx5 nucleosome structure:
./deform_energy dna_1kx5.out

-> this test is able to reproduce the results of Tolstorukov et al. (2007), J. Mol. Biol. 371, 725-738, Table 1.

- deformation energy of two identical duplexes with inverse order of strands in the PDB file:
./deform_energy gact.out
./deform_energy gact-inv.out

-> the same total deformation energy is obtained for the two duplexes as expected!

Please note that these two tests fail with the deformation energy program currently distributed on the 3DNA website at:

http://rutchem.rutgers.edu/~xiangjun/3DNA/users.html  [see the post below -- Xiang-Jun Lu (Jan. 8, 2012)]

Dr. Thomas Gaillard
BioMaPS Institute
Rutgers University
610 Taylor Rd
Piscataway, NJ 08854