|Opened on:||Friday, July 29, 2016 - 12:48|
|Last modified:||Friday, July 29, 2016 - 12:48|
I'm raised this suggestion before but perhaps its time to suggest it again in the hopes that I might gather a few recruits to the idea.
I have had a suspicion that residues of different side chains not only apply different forces, both negative and positive, but apply their influence at different times during the process of folding based on size and proximity. Several changes to the way forces are handled may happen as a result. I think we can examine some of those differences.
To do this, I would propose giving a different clashing behavior value to each of the different side chains, nineteen in all. For example, the clashing behavior tool would have a list of the side chains, ranked in order by size, positive to negative. A player could wish to examine the behavior of the protein when the largest of the side chains exert their forces while the smaller, less influential side chains have no effect. phenylalanine, tyrosine and tryptophan may be the only side chains effecting the initial folding when their clashing behavior is set to 1.0 and all of the others are set to 0.0%. Later in the same puzzle, the clashing for all side chains might be brought into play.