Sneak Preview: HIV Design Game

We are approaching a release date for our first protein design game.  In these classes of games, you will still fold  proteins, pack them in the smallest possible places, bury the hydrophobics, etc.  In addition you will be able to craft different parts of the protein in order to achieve secondary goals.  For example, an additional goal could be that the external shape of the created protein fits very nicely with a virus, or any other molecule.

You will be crafting proteins by changing the actual amino acids anywhere on the backbone, and even extending the protein sequence.  There will be a few new tools, and even some additional requirements for a successful design aside from the score.  To get you ready to make your own proteins we will be introducing new set of level puzzles specifically focusing on protein design. 

We are particularly excited about this new chapter in foldit evolution because there are practically no automated methods for protein design -- you will be primarily competing with the biochemistry experts to find the best novel protein structures.  In my view, I think foldit players will likely provide even greater advancement to science with design problems.  The best part is that each set of puzzles will be focusing on a different target, such as an HIV virus.   The best scoring proteins will then be synthesized in the biochemistry lab in order to confirm it's folding structure and the protein function.  The biochemists focusing on the specific problems will keep us all up to date with the findings.  These findings in turn will produce new design puzzles for us to work on.  Effectively, you will all be the crucial part of the scientific exploration process! 

The first design puzzle will focus on the HIV virus.  Some time around the release date, we will introduce you to the biochemist who will describe the objective, and the scientific hypothesis you will be working on.  The tentative release date is second part of March.

( Posted by  zoran 68 1814  |  Thu, 02/26/2009 - 03:54  |  10 comments )
Joined: 05/10/2008
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Very very cool

I will be very excited and proud to be a part of this next phase!  Thanks for giving us the opportunity to make a real contribution to your work.  I think it's especially cool that you will be synthesizing the result. How will you name the resulting proteins?

Joined: 11/20/2008
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Like Brad, I think the fact that the best results will be synthesized is extremely is the fact that there will be information on how things are working out!

Also, the new folding strategy ...instead of just finding the "most likely shape" of a protein, we'll be trying to mold a certain shape which simultaneously needs to score well, right?...that sounds like a big challenge, and a lot of new territory to be discovered!
I'm glad I found out about this place so I can be part of this :)

Joined: 08/05/2008
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I like doing new things and

I like doing new things and give this new Feature a definitive THUMBS UP. Looking forward seeing it...

Perzik's picture
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being in the field of protein engineering and design, I'm really really looking forward to these features!
Nice to see that the whole fold it stuff develops so fast, amazing

Joined: 05/26/2008
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You all work fast, great job making this a soon to be reality.

Can't wait to take a crack at it.

Hopefully we will have longer than 1 week for these since they will likely take a bit more playing with than just folding proteins  :)

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we do work hard, but as you

we do work hard, but as you know, we also do happen to have a few bugs here and there ;)

it is likely that the puzzles will iterate between the biochemists modifying them slightly and posing a similar puzzle once the old one expired.

zoran's picture
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we haven't figured out the

we haven't figured out the naming process, but rest assured every person contributing to the results will be fully credited.  Our primary goal is to enable you to be the creators of the new structures.

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Patent pending .... not!

I am not a lawyer. Lawyers are like beavers... the dam things up. So I'm a bit hesitant to raise this point but...

This is an exciting development. True science discovery in a totally public forum. This does present new frontiers in knowledge evolution. If a group evolves a totally novel sequence that perfectly addresses the target problem is the result patentable? Since it was developed in a public forum there may be some problems patenting it.

Interesting times...

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patent pending - not

the whole point of foldit is to democratize the process of scientific discovery.  we will always strive towards public ownership of any findings produced by the game.

Joined: 05/17/2008
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Any update on when you guys might be able to release?

I am really looking forward to this, so I thought I would just check in to see when this might be here. Thanks.

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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, Boehringer Ingelheim, RosettaCommons