Analysis of the protein-protein binding interphaces in MARTINI models
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
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@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
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@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@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
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@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@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@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
participants (2)
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Elaine Meng -
James Starlight