[Chimera-users] Query on GPI-anchor proteins

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 17 12:46:41 PDT 2015

Dear Aditya,
This sounds like a problem for which you would need other programs.  I can’t think of how you would use Chimera.  

Some approaches might be to take the set of known substrates and try to see if there are sequence and/or structure patterns in common among them, and then try to identify such sequence and/or structure patterns in your candidate substrates. Sounds like there isn’t much 3D data, and so you would probably need to look into programs for multiple sequence alignment and pattern derivation (e.g. HMMs, sequence profiles).  Although Chimera has some sequence alignment capability, it is not the first package you would go to for that type of study (especially without much 3D data), and it doesn’t create HMMs or profile outputs.

There might also be databases that enumerate known and/or predicted GPI anchor proteins, but I don’t know much about the topic myself.

I hope this clarifies,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 17, 2015, at 11:38 AM, Aditya Padhi <adi.uoh at gmail.com> wrote:

> Dear Chimera Users,
> I am working on a protein, which is known to cleave few GPI-anchor proteins (Glycosylphosphatidylinisotol). Also, I know that there are several other candidate GPI-anchor proteins which may or may not be cleaved by my protein of interest. I was wondering, if there is any tool/method in Chimera using which I can atleast get some preliminary information on which of the proteins that could be probably cleaved by my protein of interest.
> The 3D structure of my protein of interest and most of the GPI-anchor proteins is not available. I was therefore wondering if there is any such tools/methods available that I am missing using which I can find out which of the GPI-anchor proteins are being cleaved.
> Any suggestion/guidance would be highly appreciated. 
> Thank you so much,
> Aditya
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