Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL

Author Topic: Stacking parameters  (Read 2278 times)

Offline spoblete

  • Verified Member
  • *
  • Posts: 2
    • View Profile
Stacking parameters
« on: December 27, 2018, 01:54:48 pm »

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.


Offline xiangjun

  • Administrator
  • Verified Member
  • *****
  • Posts: 1528
    • View Profile
    • 3DNA homepage
Re: Stacking parameters
« Reply #1 on: December 27, 2018, 02:08:45 pm »
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,

Dr. Xiang-Jun Lu [律祥俊]

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite


Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.