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

Elaine Meng meng at cgl.ucsf.edu
Sun Nov 26 09:17:06 PST 2017


Sorry, I don’t know of any tricks specifically for coarse-grained models.  

I would try turning OFF the “Include intra-molecule contacts,”  if you haven’t done that already (since you said “inter-molecular” I wasn’t sure if that was what you meant).  However, it may be that molecules within your coarse-grained models are not recognized as molecules in Chimera.

Elaine

> On Nov 23, 2017, at 1:47 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> Thank you for the suggestions, Elaine !
> 
> I have already tried "Find Clashes/Contacts" plugin. In generally, it
> works good, however its application on more complex oligomeric
> patterns (e.g if I deal with 10-20 GPCRs in one system) is a bit
> complicated. Briefly, if I select only one monomer and than try to
> find its contacts with the rest of the atoms ( I have changed the
> contact threshold to -1.2 for the MARTINI) - it works fine. However,
> If I selected all of the atoms (even excluding inter-residue and
> inter-molecular contacts) and changing the search criterium "against
> themselves" - it found alot of contacts within the monomers. Does
> anybody use any tricks for the MARTINI models to fascilitate the
> contact searching?
> James
> 
> 2017-11-22 17:52 GMT+01:00 Elaine Meng <meng at cgl.ucsf.edu>:
>> 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
>> -----
>> 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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