[Chimera-users] Analysis of the protein-protein binding interphaces in MARTINI models

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 22 08:52:20 PST 2017

Dear James / Gleb,
This question seems too broad, perhaps.  I don’t know that much about MARTINI, so I’m guessing instead of atoms you just have a bunch of points that each represent multiple atoms.  In that case you could probably use any analysis that does not directly use exact atomic locations, atomic radii, or atomic point charges.  Analyses that DO use those things include surface-area calculations, Find Clashes/Contacts, FindHBond. 

Maybe you should just first think about what Chimera analysis you want to use, then just try it on your GC model and see if it works rather than trying to get some exhaustive list of what might work.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 22, 2017, at 2:23 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> Dear Chimera users!
> I would like to make some analysis of the protein-protein binding
> established in coarse-grained MARTINI simulations. Briefly Chimera has
> recognized a coarse-grained pdb file of 16 martini models of GPCRs.
>  What Chimera tools (e.g. contact maps, clustering of interphaces)
> should work with CG models? What tricks should be used to make this
> analysis easier? Because I am working with several proteins in one
> system, I would like to work with its CG models without the conversion
> to all atomistic representations.
> I thank you so much for the help!
> James

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