Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › Docking prepack vs. relax
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Anonymous.
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February 21, 2017 at 1:37 pm #2587
Anonymous
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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February 21, 2017 at 3:58 pm #12151
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.
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February 21, 2017 at 3:58 pm #12672
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.
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February 21, 2017 at 3:58 pm #13193
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.
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