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Questions and answers => DNA/RNA-protein interactions (SNAP) => Topic started by: akakios on December 06, 2020, 09:09:17 pm

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Title: Difference between pi-stacking and pi-pair in SNAP
Post by: akakios on December 06, 2020, 09:09:17 pm
Dr. Xiang-Jun Lu,

Thank you for the amazing software. I am using it for my research.
I tried to find the definition of pi-stack and pi-pair in the output of SNAP but
could not find it.

Could you tell me the difference or the docs describing about it, please?

Takayuki Kimura
Ph.D. candidate, Tokyo Institute of Technology
Title: Re: Difference between pi-stacking and pi-pair in SNAP
Post by: xiangjun on December 07, 2020, 08:01:08 am
Hi Takayuki Kimura,

Please clarify your question by providing concrete examples of "pi-stack and pi-pair" in relation to SNAP output.

Thanks,

Xiang-Jun
Title: Re: Difference between pi-stacking and pi-pair in SNAP
Post by: akakios on December 07, 2020, 11:09:51 am
It is about the two sections around the end of SNAP outputs Like below:
Pairs and stacks. Thank you.

****************************************************************************
List of 7 base/amino-acid pairs
       id   nt-aa   nt           aa      vertical-distance   plane-angle
   1  1oct  A-gln  A.DA204      C.GLN44         0.05             
****************************************************************************
List of 2 base/amino-acid stacks

Title: Re: Difference between pi-stacking and pi-pair in SNAP
Post by: xiangjun on December 07, 2020, 12:33:28 pm
The base/amino-acid pairs identified by SNAP are named pseudo pairs (see doi: 10.1093/nar/gkr452). I have never heard of the term "pi-pair" as used in the your initial message. So I was confused as to what it really means.

Using 1oct as an example, a graphical illustration of the A-gln pseudo-pair (A.DA204 and C.GLN44) is attached. It should be clear that it is indeed like a base pair (H-bonds, coplanar).

Please generate a similar graph of a base/amino-acid stacking interaction and post it back. This way you would better understand the differences between the DSSR output sections on pair vs stack. It also helps other viewers of the thread.

Best regards,

Xiang-Jun
Title: Re: Difference between pi-stacking and pi-pair in SNAP
Post by: akakios on December 07, 2020, 05:01:24 pm
Thank you for the clarification. Stack example is like the following:

***************************************************************************
List of 2 base/amino-acid stacks
       id   nt-aa   nt           aa      vertical-distance   plane-angle
   1  1oct  T-gln  A.DT203      C.GLN44         3.79              1
   2  1oct  G-arg  B.DG225      C.ARG105        3.31       
Title: Re: Difference between pi-stacking and pi-pair in SNAP
Post by: akakios on December 07, 2020, 08:00:00 pm
Dr. Xiang-Jun Lu,

Maybe now I got what I wanted to know. I appreciate it. Thank you.

Takayuki

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University