28 Mar
2007
28 Mar
'07
12:49 p.m.
Hello all,
I am generating models for a strained protein chimera using weakened restraints on one of the two domains, to see if Modeller will unfold the domain to relax the mechanical strain. I have weakened all Ca-Ca and N-O distance restraints (roughly 3,800 out of 16,500 total restraints) by a factor of 100, but it had nearly no effect on my output models. Is there something fundamentally flawed with this approach? Are there other specific restraints that might be recommended for weakening, or would it be best to simply weaken all restraints associated with the targeted domain?
Thanks in advance!
Sincerely, Brandon Mills
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Brandon Mills
bmm25@pitt.edu
(814) 360-1382
Lab: 338, Eberly Hall