normal Go-MARTINI3 and protein protein interactions

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8 months 1 week ago #9691 by shaukat_i
Hi everyone,

I am simulating a soluble protein (monomer, ~400aa). I hope to further understand the dimerization of this protein. I came across the GoMARTINI implementation for sampling conformation dynamics of the proteins using martini. Can I extend the approach to understand dimerization as-well? Is the aggregation propensity taken care of for soluble proteins in martini3 with Go potentials?

Thank you in advance.

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7 months 3 weeks ago - 7 months 3 weeks ago #9697 by adolfom
Replied by adolfom on topic Go-MARTINI3 and protein protein interactions
I think one can apply GoMartini for each protein chain and between them is right away the best solution. You can use the server ( pomalab.ippt.pan.pl/GoContactMap/ ) for contact map determination and include as well the contacts between both protein (chain A and B, as it was done in the ref. doi.org/10.1021/acs.nanolett.1c03584 . Also you should check the best epsilon for your model.
Best,
Adolfo Poma
Last edit: 7 months 3 weeks ago by adolfom. Reason: missing key reference

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