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Design strategy - One chain at a time OR two chains together?

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Design strategy - One chain at a time OR two chains together?
#1

Hello folks,

this is a conceptual question.

The protein I am working with has 2 domains (2 chains), and I would like to redesign part of the surface of each domain AND the interface between those domains.

I see two possibilities here (maybe there are more):

Option #1- Break the design into three smaller problems - i.e., design only chain A, then design only chain B, and finally, design the interface (5 residues + 7 residues  + 11 residues).

Option #2- Design all residues at the same time (23 residues).

I am planning to redesign the residues and restrict repacking to only the neighbor residues; I wonder what is the best tradeoff between search space, computing time and accurate conformations.

 

Can you please advise on that?

Thanks in advance.

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Wed, 2022-01-05 18:19
tlopes