Possible Rebuild tool optimization

Case number:845813-991098
Topic:Game: Tools
Opened by:scottyler89
Opened on:Tuesday, November 15, 2011 - 06:04
Last modified:Friday, November 18, 2011 - 04:46

I noticed that when rebuilding a section with constraints, rebuilds that wildly violate the constraints are still considered (yet rarely used - because of the constraint modified boltzman factor). I'm guessing that this tool is a modification of the monte carlo method, but perhaps it might be more efficient, computationally, to eliminate GUI visualization of the least favorable conformations (unless it's one of the few times that a very unfavorable conformation is indeed randomly selected).

(Tue, 11/15/2011 - 06:04  |  1 comment)

Joined: 08/09/2010
Groups: foldeRNA

In other words, I think there should be an "if" statement within the rebuild tool looking at the selected residues to look for constraints. If true - then GoTo the routine for constraint modified energy calculation, and use the constraint modified Energy for the B.F. calculation.

Does that make sense?


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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