(Mon, 09/13/2021 - 19:30 | 4 comments)
How does Foldit decide which residues are in the core?
|Opened on:||Monday, September 13, 2021 - 19:30|
|Last modified:||Friday, September 17, 2021 - 22:48|
I have a design that keeps giving 0's for the Core Existence: Monomer and Core Complex Objectives. If you check the Show box for one of these Objectives, each segment appears blue (protein exterior), green (border between exterior and core), or orange (core). I think the # of orange (core) residues determines the scores for the Core Objectives. That being said, how does Foldit decide which residues to color blue vs green vs orange? Does Foldit use the Packing or Hiding subscores for each residue? Does Foldit consider the # of voids near each residue? Does Foldit consider how many hydrogen bonds each residue has or how many BUNS are near the residue? Does Foldit consider the hydrophobic vs hydrophilic nature of each residue? For example, are the amino acids vwylmpiacfg (orange in the Selection Interface's Mutate Tool) more likely to be treated as core residues than the amino acids stnqrhkde (blue in the Selection Interface's Mutate Tool) ? The amino acids w & y are odd in that they are colored orange in the Mutate Tool even though they can form hydrogen bonds. Are w & y more likely to be in the protein interior or on the surface of the protein? If there are web pages or articles that answer these questions, please post links here. Also, if there are recipes folks have found helpful for raising the Core Objectives' scores, please let me know. Thanks, Jeff