Does the Rebuild Tool depend on the initial state?

Case number:845813-2006342
Topic:Game: Tools
Opened by:jeff101
Opened on:Wednesday, December 26, 2018 - 09:24
Last modified:Thursday, January 3, 2019 - 20:29

Say you have a protein structure scoring 9000.000 and select its
residues 30-40 for rebuilding. After the 1st rebuild, you have a
score of 5800.000. At this point, what has a better chance of
giving you a good-scoring rebuild of residues 30-40: starting
from the structure with score 9000.000 or starting from the
structure with score 5800.000? Does rebuild only care about
the endpoints of residues 30-40, their sequence, and their
assigned secondary structure, which should be the same for
both scores 9000.000 and 5800.000, so both starting structures
should have the same chance of giving a structure with a score
of 9300.000 when residues 30-40 get rebuilt?

Also, does rebuild's results depend on the wiggle power or
clashing importance settings? What settings give the best
chance for a good-scoring rebuild?


(Wed, 12/26/2018 - 09:24  |  1 comment)

bkoep's picture
User offline. Last seen 21 hours 36 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

No, the structures returned by Rebuild do not depend on the initial score. The Rebuild algorithm only depends on the endpoints of the selection, their sequence, and assigned secondary structure.

I don't believe wiggle power or clashing importance will have any impact on the structures returned by Rebuild.


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