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Tlaloc's picture
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I was invited the University of Washington today and met with Zoran Popović, Firas Khatib (Beta_Helix), and David Baker. We discussed a number of things in the time I had there. One thing that came up with David Baker was about how to improve the information about foldit that is available. I told him that I'd at least try to form the list of questions that need answering.

This is a chance to improve much of the information available on the wiki. So here is your chance to ask questions about things related to the biology in foldit. You ask it, and we'll try to get some answers out of the foldit guys.

Just to give you an example of the kind of question I think we might get answered:

What does rebuild actually do? As I understand it, it looks at a database of segments from proteins with known native structures and tries to find segments that fit the sequence of amino acids and the endpoints of the rebuild. How exactly does that work? Where does that database come from? Who maintains it? Is it being added to as more natives are determined? Is it hardcoded into the program or downloaded from the server (i.e. can it change frequently or at all?)? Is this even the correct understanding?

Ask away, and we'll try to get the questions answered using words that a non-biologist, like me, can understand.

NinjaGreg's picture
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Joined: 05/21/2010
Groups: Go Science
Rebuild operation

If I isolate five segments with frozen segments and launch a rebuild, stop the rebuild, undo to the starting point of the rebuild, and restart the rebuild, will it just repeat all the positions from the initial run? Or will it generate a different sequence of positions?

Joined: 08/09/2010
rebuild operation

Try it and see. You can use the undo graph to make a record of the scores of the different poses. Then repeat from the start point. I suspect you will find that the scores are different - hence the poses are different. I know that you can run a rebuild script twice on the same starting save and get two different results.

Joined: 09/18/2009
Groups: SETI.Germany
Iterations

What exactly is one iteration when perfoming wiggle/shake?
Sometimes, a wiggle using one iteration does much, sometimes almost nothing.

Joined: 08/09/2010
Game tools - mutate sidechains

What exactly does this tool do? I know it can change the identity of (mutable) sidechains from one amino acid to another. But I have seen it raise my score even when no amino acids are changed. I would like to have greater knowledge so it can help my intution in the use of tools - I would like to know how they all work.

Joined: 08/09/2010
rebuild tool

I'd like some more info on what this tool does. It seems to have some random component, since you can run a rebuild script twice on the same starting save and get different results. It seems to be "clever" in that if you leave in structure and add bands on sidechains, it will try to give poses that preserve your structure and shrink your bands. But I suspect that when run on a selection that is all loops, it just gives random poses that start and end at the endpoints (roughly speaking: of course the end segments and those adjacent bend and twist, but the point is that the rebuilt shape connects up with the protein). I'd like to know if it is just working completely randomly within these constraints, or if when you run it for a long time and let it generate many poses it is applying some algorithm to search for some shape (I suspect not, but I'd like to know). Similarly, I'd like to know if it takes any account of sidechain positions when generating poses (again I suspect not). It would be nice to have some more control over the rebuild poses since at present there is no guarantee the tool will ever give you a pose in the right shape you are looking for.

Joined: 08/09/2010
Importance of FoldIt

Is the importance of FoldIt merely conceptual for chemists, or can the FoldIt results be used in understanding of actual proteins? If the latter, how and how can FoldIt players provide more useful feedback to chemists and vice versa? Does it matter how many moves we use in folding proteins and whether we use scripts? Do chemists prefer many different solutions or just the highest-scoring fold, and why?

Joined: 09/16/2010
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recipe editor

Ask if there is any commitment to improving the recipe editor. Particularly the Linux version without the copy/past facility is onerous and nearly useless.

Joined: 09/02/2010
Groups: None
Other questions...

What are the uses for the secondary structure in Foldit. I would guess: to make a difference between backbone wiggle and wiggle all. There are other, probably correct suggestions in the Wiki, but really what does it do? In actual proteins these structures do have different behaviour. For example the alpha helix tends to destabilise because of charge build up. Is this effect incorporated in the calculations, and if it is, is it dependent on the choice of the secondary structure?
Game related: what does clashing importance do? I found al lot of hits on this in the Wiki but an explanation did not immediately appear.
In general I would suggest to extend the descriptions of the Foldit functions in Lua. It was not apparent to me that the select function can select multiple ranges by applying it more than once. This good behaviour of cause, but it surprised me when I found out. I think it should be in the documentation...

Joined: 10/29/2010
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agree!

I agree with apple.muncy, Linux without the copy paste facility is worthless...just my 2 cents!

kpinvt's picture
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Joined: 08/21/2010
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Browser Based Fold-it

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's picture
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Hopefully answers here

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.

beta_helix's picture
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Hanto, try asking in the feedback:

http://fold.it/portal/feedback

I searched the feedback for your username and did not see any posts about your problem.

Hanto's picture
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Apologize for negative vote.

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.

Brick's picture
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Hanto - Use FEEDBACK

As beta_helix suggested, please use FEEBACK to ask your question. That is the proper place to ask for help and support. The FORUM is more for discussions about - things.

http://fold.it/portal/feedback

Joined: 08/11/2010
What do Segment Information numbers mean?

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.

Joined: 08/11/2010
Segment Information

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.

Joined: 08/08/2010
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Custom proteins

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?

beta_helix's picture
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playing around with custom proteins

You can do this by creating a Contest:
http://fold.it/portal/node/add/contest

and selecting the "Freestyle Design: Variable Length" Puzzle

You can then add & delete residues and mutate the Alanines to whatever you want them to be. Enjoy!

Joined: 12/04/2010
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hm... mutate sidechains

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?

Joined: 01/12/2011
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expanding the protein

i see all kind of recipes that compress the protein structure and mutate it, but none that expand the protein ... how do i find a recipe that pulls an overly compressed protein apart?

Joined: 06/17/2010
Try

Tlaloc Push
mine Push
GA Bands 1.8 have also "push" option, you can enable it and disable all other.

Joined: 09/18/2009
Groups: SETI.Germany
Problem...

...is, that there is an in-game band length limit of 20, so you can only push segments apart which are close enough to each other, so you can't do a long push or turn compressed puzzles to a denovo puzzle with only one band.

rav3n_pl, Tlaloc, some others and me already asked about increasing the maximum bandlength via feedback suggestions.

Joined: 03/20/2011
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New Puzzles

I don't understand puzzle selection. It seems like all the puzzles that have more than one contestant are closed or inactive. I don't know if any of this is helping with real science so I'm stuck just competing. I would like competition on more than beginner stuff. Help

Also once you select something other than the impulse buy (405,407,408) at the first display of the main menu there seems to be no way to get back to that choice without quiting foldit and restarting it. Is there?

I would really rather compete with a puzzle that will actually do some good.

beta_helix's picture
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maybe you should start here:

Maybe this post can help you: http://fold.it/portal/node/988864

In it you can see that you can always select "Puzzle Menu" in the Menu Tab.

You can see that (other than the Beginner Puzzle) you can try puzzles advanced puzzles 409 and 410.

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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