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-no_filter flag in docking

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-no_filter flag in docking

what does it do? thanks.

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Tue, 2013-05-28 11:58

I'm not familiar with the Rosetta++ docking protocol, but if it works like the -no_filter flag in Rosetta3 docking (probably a reasonable but possibly inaccurate assumption), it turns off the various quality filtering that the docking protocol performs on potential docked structures.

According to the Rosetta3 source code comments, in the centroid stage this would be "Checks (1) at least some contact is being made between docking partners, (2) clashes are limited so partners are not overlapping and (3) constraints, if present, are met." In full atom stages it's "(1) total_score beats the cutoff given (2) interface_score must be negative" There's also a notation that Rosetta++ also has "1-score filter 2-fa_rep filter 3-interfaceE filter 4-chainbreak filter" that Rosetta3 does not (yet) have.

Hopefully that gives you a sense of what's involved, but be advised that details may be different.

Tue, 2013-05-28 18:58

thank you

Wed, 2013-05-29 10:26