Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing
· Video Overview· RNA Covers
-
Greetings.
I would like to know more specifically the parameters used in the base-stacking classification. I have seen that some almost-perpendicular pairs of bases are annotated as stacked, so I would like to know if the criteria is based uniquely on the hull overlap or if they belong to a more specific perpendicular stacking interaction set.
Many thanks in advance.
Simón.
-
Hi Simón,
Thanks for using DSSR and for posting your questions on the Forum.
You've touched a subtle, technical point. In DSSR, stacking is decided by no-zero overlapping area of (extended) base-rings projected on the mean plane of the two base normals. The two bases may be (nearly) parallel and stack well, or they are offset, and at a big angle. So being 'stacked' are not equal, as reflected by the different overlap areas and the angles. Users can filter the DSSR-derived stacks based on these two parameters.
These are just general comments. If you provide some specific examples, we can discuss in more detail.
Best regards,
Xiang-Jun
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.