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Questions and answers => RNA structures (DSSR) => Topic started by: spoblete on December 27, 2018, 01:54:48 pm

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Title: Stacking parameters
Post by: spoblete 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.

Title: Re: Stacking parameters
Post by: xiangjun 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,


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.