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

James Starlight jmsstarlight at gmail.com
Mon Dec 4 05:37:09 PST 2017


One question regarding Find Clashes/Contacts.

assuming that I have assigned the unique letters for each of the monomer
 in my CG system. Now I am using this selection ("the individual
chain" vs "all other systems") to calculate contacts using -2.2 cutoff
for MARTINI (operating with the backbone atoms only). Is it possible
to run the same routine in batch mode i) for the individual pdb as
input as well as ii) for the md trajectory (to calculate occurence of
the contacts along the trajectory)? I would be very grateful for some
example script file for batch Chimera!

James

2017-11-27 12:03 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> 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.
>
> James
>
> 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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