Get answers to your questions about foldit

Started by Tlaloc

kpinvt Lv 1

I usually have some down time at work where I would love to be able to play this game. The main problem is I can't download or install software. Will there ever be a completely browser based version of the game?

Hanto Lv 1

Since almost no reasonable answers are being given in the main forum, I think I will try this thread and see what the experts know. Gentlemen and Ladies or vice-versa as the case may be, I have a situation on this laptop that should be easy to answer for some of you. There used to be some start parameters for Fold.IT that were absolutely required by this laptop, else there would be no display whatsoever. I had this problem before and researched it and finally found the answer on a website that has long disappeared now, i.e. I have been looking for almost two months now with no agreeable results. I know the answer is extremely simple because I have the same laptop and the same problem but don't remember the exact parameters involved and can't for the life of me find ANY mention of any start parameters for Fold.It at all these days. Surely they have not become totally extinct…
Thanks for any attention to this issue that might be forthcoming.

Hanto Lv 1

Apparently I voted negatively unintentionally on that reply. Sorry about that. Look at page 2 of this forum. Question has existed since 9/22/2010 without a single reply.
When I did find the correct answer/s for this issue, it was on a site that that obviously to me at least probably didn't have long to live. I can't find the support forums either, and quite obviously from comments made in other places in this forums, others are having similar issues.

I am totally amazed by the fact that in my first problem with this issue, the answer was not found on this website or any major website associated with Fold.It and now, probably two years later, there is still nothing to be found. I guess if I ever do find the correct answers again, I will have to ask someone here to make them into a sticky.

Thanks again.

John McLeod Lv 1

I found some hints here
http://foldit.wikia.com/wiki/Get_segment_score_part

the PDB# is maybe "protein database number" for the number of the amino acid in the puzzle file. Seems to be same as the number at top line to left of AA/sidechain type. Ever different?

Reference (last at bottom) from above link seems to be "relative hydrophilicity" with hydrophobes getting negative values (constant for AA type).

Others slightly intuitive – On a sample of one, "Score" seems to be sum of next six (all except Reference), that right, assuming rounding errors? Is puzzle score sum of all these segment scores?

Descriptions of how the the game sees Clashing, Packing, Hiding, Bonding, Backbone, Sidechain and where the scores from these come from would be appreciated.

John McLeod Lv 1

regarding above, that's the box that you get if you mouse-hover over a segment (AA) in the protein and hit Tab. One of the many Easter Eggs I found studying and puzzling over the Help screen.

paramecium13 Lv 1

Is it possible to submit a custom made protein sequence to rosetta or foldit and get the structure or insert it into the foldit program to play aroung with?

fractalman Lv 1

hm…
mutate sidechains checks to see if changing the amino acid can improve your score, but since it also checks several positions for each, it may sometimes end up shaking a sidechain without actually mutating it.

rebuild: i'm not entirely sure what algorithm it uses…but I have observed these:

  1. It tries to turn helixes into actual helixes, and tries to leave sheets more or less straight.
  2. It is very ignorant of sidechains (and thus terrible for proline segments)
  3. It likes to make hydrogen bonds. It sometimes seems to pay attention to sidechain-backbone bonds, maybe sidechain-sidechain bonds as well, though the latter are hard to be sure about.
  4. It seems to pick a small number of backbone segments to randomly alter, and will either move the protein or not move the protein to the considered position.
  5. Did i mention it doesn't work well with prolines?