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

James Starlight jmsstarlight at gmail.com
Mon Nov 27 03:03:16 PST 2017

Thank you so much for the suggestions, Elaine!

Indeed, I have turned off the both flags but the intra-models contacts
are still recognized.

it seems that in order to determine carefully the per-residual
contacts between monomers, I should to make a backmapping of the CG
models to AA.


2017-11-27 9:23 GMT+01:00  <sdimicco at unisa.it>:
> Grazie mille
> Il 2017-11-23 04:47 James Starlight ha scritto:
> 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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