toshiue's picture
User offline. Last seen 2 hours 44 min ago. Offline
Joined: 01/31/2016
Groups: Go Science
client scoreboards not updating

client scoreboards not updating, have heard the same from three other group members.

Susume's picture
User offline. Last seen 9 hours 57 min ago. Offline
Joined: 10/02/2011
"Satisfied" red and blue atoms

From the H-bond network puzzles we learned the idea of bondable atoms being "satisfied" if they have H bonds. I assume that idea also holds in the ligand puzzle (in theory, if not in the score).

I have a choice of histidine or lysine in one location to bond to a red atom of the ligand. Foldit gives better score to the histidine, but it removed a threonine that I had put in to "satisfy" the red atom of the histidine, so now I have a mostly-buried red atom that is "unsatisfied." If I put the lysine in, its one bondable atom bonds to the ligand, but it's only one bond - seems like sometimes lysine forms up to 3 H bonds. In sphere view, neither the HIS nor the LYS are very accessible to water.

Is a histidine satisfied if its blue atom is H bonded and its red one is not?
Is a lysine satisfied if its blue atom has only one H bond?

Foldit doesn't seem to penalize unsatisfied buried atoms or to reward satisfied ones, and it's frustrating trying to guess what will work. Is there some way the score (or some other feature) could be used to give us feedback on this? It seems like it will always be an issue in ligand puzzles.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons