Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: Which residues does SNAP define reference frames for?  (Read 3037 times)

Offline jms89

  • regular
  • *
  • Posts: 10
    • View Profile
Which residues does SNAP define reference frames for?
« on: August 02, 2018, 07:29:39 pm »
Hello, since there's no paper for SNAP yet (you should write one at some point!), I'm just going by my experience with the program and this forum. As I understand, pseudo-pairing and stacking interactions are identified based on geometric criteria between a planar moiety which defines the amino acid reference frame, and the standard base reference frame. So these are plane-plane interactions.

My question is, for which residues exactly are reference frames defined? Does every amino acid (perhaps except alanine and glycine) have a defined reference frame? So can any residue participate in pseudo-pairing and stacking, or does SNAP only identify these interactions for a subset of amino acids?

Thanks.

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1328
    • View Profile
    • 3DNA homepage
Re: Which residues does SNAP define reference frames for?
« Reply #1 on: August 03, 2018, 10:40:45 am »
Thanks for the encouragement for writing a paper on SNAP -- it's been on my to-do list for a while, but delayed for various reasons. Overall, I take it as a positive thing that a method paper is written after that corresponding program has been in active use for a while. My goal here is not to write a paper but to solve a set of related problems so that the community can build upon my work.

You are right in that pseudo-pairing/stacking interactions are between planar moieties in proteins and the standard base reference frame. The planar moieties include the amino-acids { "arg", "phe", "tyr", "trp", "his", "asn", "asp", "gln", "glu" } and the peptide bond. A reference frame is defined for each of them. The pseudo-pairing/stacking interactions of these planar moieties with nucleobases are identified and quantified using exactly the same algorithms as in 3DNA/DSSR. In addition to the pair-wise interactions, 'multiplets' and stacks (as in DSSR) involving both amino-acids and bases will be reported in future releases of SNAP.

HTH,

Xiang-Jun
« Last Edit: August 03, 2018, 11:42:02 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline jms89

  • regular
  • *
  • Posts: 10
    • View Profile
Re: Which residues does SNAP define reference frames for?
« Reply #2 on: August 06, 2018, 03:40:00 pm »
Great, thanks for the info!

 

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.