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Docking prepack vs. relax

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Docking prepack vs. relax

Is Docking Prepack simply a specialized version of Relax for dealing with complexes? (separate complex, minimize sidechains, reassemble)

If I am docking proteins A and B where each has already been individually relaxed, is there any need for running Docking Prepack on the PDB file that contains both relaxed A and B, already oriented correctly for local docking?

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Tue, 2017-02-21 05:37
David Weis

If the monomers are pre-relaxed, you can skip prepack.

It's a problem of false attractors in the conformational space.  To improve speed, docking only repacks residues near the protein-protein interface.  If one monomer has a bad local clash caused by a bad rotamer, docking is encouraged to find interfaces near that bad rotamer, so that it has freedom to repack it, causing a large improvement in that monomer's energy and a Monte Carlo accept of an otherwise wrong structure.  Prepacking removes these issues so that hopefully the only energy well in the landscape is the real docked structure.

I believe prepack is set up to flex only the degrees of freedom that docking itself also flexes - I think it samples far less than relax does.

Tue, 2017-02-21 07:58