4 replies [Last post]
Joined: 06/22/2010
Groups: Wiscofolders

Do most puzzles start with a fully unfolded protein (long chain)?

It seems that of the puzzles that are available (there aren't any beginner ones, it seems) are fully unfolded. But many of the "suggested methods" on the Wiki suggest global wiggle/shake as the first move (http://foldit.wikia.com/wiki/Pletsch's_Suggested_Method). This just seems to kinda bend the big long chain.

Are these puzzles best started with the alignment tool? Are the suggested methods for proteins that are already kinda folded?

Thanks for the help.

-sean

Joined: 06/26/2010
Groups: None
Beginner Puzzles

I am having similar issues could anyone provide us with some guidance

Joined: 06/17/2010
Use anligment tool to plan

Use anligment tool to plan molecule and push happy face on left to start thread and create it.
If anligmend is "good" you get molecule to work, if to many "errors" in templace U see "cant thread" meassage and "bad" parts in aligmend will flash red few times.

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

...those plain, unfolded long chains are best processed with the alignment tool first.
Anyway, you can twist an unfolded one "by hand", but this is kinda tricky and takes a lot of time, especially the long ones.

Joined: 05/09/2008
Groups: None
you are right sean

Lately, most CASP9 puzzles have all been Template Based Puzzles where you need to use the Alignment Tool:
http://foldit.wikia.com/wiki/Alignment_Tool

Just in the past few days, however, the CASP9 organizers have released the first targets in the Refinement Category:
http://predictioncenter.org/casp9/targetlist.cgi?view=refinement

For these Refinement targets, they give us a prediction which is close to the native that we need to refine.
(The model given to us is a prediction that was submitted by a server or human group for a past target that has already expired)

So once we post these Refinement puzzles, you will be starting with 1 nice looking protein and you will need to make it even better! So all the suggested methods and info on all the wikis will be very applicable to this!

We hope to have the first Foldit Refinement Puzzle up in the next few days, we are still trying to figure out how to fit them in with all the puzzles you already have to work on. We don't want to overwhelm you with CASP puzzles!
The good news is that there will be no more prediction puzzles after July 31st, only Refinement puzzles!

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