What is the best way to use AlphaFold in Foldit puzzles?
|Opened on:||Saturday, August 28, 2021 - 17:14|
|Last modified:||Tuesday, September 7, 2021 - 05:00|
At https://fold.it/portal/node/2011929#comment-45091 argyrw wrote:
question for deep mind
Hi! we want only statistic 80% in the confidence and similarity or
we want max points of the foldit with that similarity and confidence.
it's necessary have max points or the important is that statistic?
argyrw has been asking similar questions in Group and Vet Chat,
but I don't know how to answer these questions. We have already
done 4 puzzles with AlphaFold, and another will finish on Aug.31.
Can you tell if we are using AlphaFold correctly? argyrw says it
is easy to get solutions with high confidence and similarity, but
they often give low Foldit scores. Is it better to focus on Foldit
scores, or is it better to go for high confidence and similarity?
My sense is that we want high Foldit scores for structures that
are very similiar to what AlphaFold would predict, so I guess if
your high-scoring Foldit solution gives low similarity vs what
AlphaFold predicts, you should try mutating the protein until
AlphaFold's prediction matches it better. This may mean using
more malek residues in sections you want to be helical. It may
also mean doing conservative mutations, like replacing certain
hydrophobic residues with other hydrophobics and replacing
certain hydrophilic ones with other hydrophilic ones.
I would appreciate it if Foldit players and staff would respond
to this Feedback with what they think is the best strategy to
use. Also, if someone on the Foldit staff would examine argyrw's
results and message argyrw directly with advice for doing better,
I would appreciate it.