Messages

1

DNA/RNA-protein interactions (SNAP) / Re: Difference between pi-stacking and pi-pair in SNAP

« 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

2

DNA/RNA-protein interactions (SNAP) / Re: Difference between pi-stacking and pi-pair in SNAP

« 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       

3

DNA/RNA-protein interactions (SNAP) / Re: Difference between pi-stacking and pi-pair in SNAP

« 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

4

DNA/RNA-protein interactions (SNAP) / Difference between pi-stacking and pi-pair in SNAP

« 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