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general question about protein docking

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general question about protein docking

I am wondering what's the general steps for Rosetta protein docking. I found there are two methods people usually use for protein docking by rosetta:

Method one:
low resolution docking(only backbone)-->cluster-->high resolution docking

Method two:
low resolution docking(only backbone)-->cluster--> relax (add sidechain with full atoms)-->high resolution docking

I am wondering which one is much more reliable?

Thank you very much

Post Situation: 
Mon, 2010-12-13 23:26

typically we do not cluster until after the high-resolution stage.

also typically we start with fixed backbone docking (ie do not relax) because the relaxation introduces a lot of noise in the scoring making discrimination difficult. See the JMB paper by Chaudhury about flexible backbone approaches to see the methods we like best. These treat the decoys equally and match appropriate scoring strategies.

Mon, 2011-03-28 08:50