Loop fix?
| Case number: | 699969-2011851 |
| Topic: | General |
| Opened by: | alcor29 |
| Status: | Open |
| Type: | Suggestion |
| Opened on: | Friday, July 9, 2021 - 20:49 |
| Last modified: | Sunday, July 11, 2021 - 05:31 |
How about making the "penalty" for bad loops MUCH bigger so scripts don't mess up the good loops we started with?
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Sun, 07/11/2021 - 05:31
#2
I think it would also help to have the Ideal Loops filter penalty
depend on the # of segments that are in non-ideal loops. This way
one non-ideal loop containing 14 segments would have a larger
penalty than one non-ideal loop containing 10 segments or two
non-ideal loops each containing 3 segments. Having the penalty
depend on the # of segments that are in non-ideal loops would
help recipes fix non-ideal loops in a more gradual and incremental
manner.
Please see the comments below for more details:
https://fold.it/portal/node/2005262#comment-41271
https://fold.it/portal/node/2005262#comment-41273
This is certainly an interesting idea! I would expect, though, that the amount of the penalty was not chosen at random.
Would it help to have a setting like "ideal loop importance", that you could set to a value ("much") greater than 1? (Without increasing the +500 points in the ideal situation, of course ;-)
Having said that, I don't think it is the script that messes up a good loop. The way I look at it (disclaimer: without having a background in biochemistry!), it is hydrogen bonds and hydrophobic interaction that act on the helices or sheets adjacent to the loop, and sometimes pull them in the wrong direction. A higher penalty might stop a recipe in its tracks, but it will not change the tendency of that section of the protein to move in the "wrong" direction.