3DNA Forum

Questions and answers => MD simulations => Topic started by: xroxzero on November 20, 2017, 11:36:51 am

Title: Analysis of major groove and minor groove
Post by: xroxzero on November 20, 2017, 11:36:51 am: Hi

About the analysis of major groove and minor groove , in this website ,
http://do-x3dna.readthedocs.io/en/latest/dna_class_api.html#dnaMD.dnaMD.DNA.set_major_minor_groove ,
it said that "The major and minor grooves (direct P-P) cannot be calculated for first and last two base-steps" .

Does any one know the reason why major and minor grooves cannot be calculated for first and last two base-steps ?

Thanks a lot
Title: Re: Analysis of major groove and minor groove
Post by: xiangjun on November 20, 2017, 12:00:07 pm: In 3DNA, the algorithm for characterizing minor and major groove widths of a DNA duplex is based on the 1998 JMB paper of El Hassan and Calladine, as shown below:

Quote
Minor and major groove widths: direct P-P distances and refined P-P distances
which take into account the directions of the sugar-phosphate backbones

(Subtract 5.8 Angstrom from the values to take account of the vdw radii
of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

More specifically, the "Appendix: Calculation of Major- and Minor-groove Widths" which is included in the 3DNA distribution ($X3DNA/doc/groove-widths.pdf). See 3DNA v2.x source code, if you want to get to the bottom of this issue.

HTH,

Xiang-Jun