The Baker Lab tests Foldit player-designed proteins

The Baker Lab has recently ordered materials to construct a batch of Foldit protein designs in the lab! We will express and purify the proteins from bacteria culture. For those proteins that we can successfully produce and isolate, we will conduct experiments to measure stability and solubility. If a designed protein is exceptionally well-behaved, we may be able to determine its native structure at atomic resolution.

Our process for selecting Foldit designs was as follows:
First, Baker Lab scientists visually inspected top-scoring and "Scientist-Shared" player designs for their favorite folding candidates. For the most part, these are well-ordered, contain significant secondary structure, have a well-packed and hydrophobic core, and also include enough complexity to demonstrate significant design.

These designs were then queued for ab initio folding predictions with the Rosetta@home distributed computing project. Computer power from volunteers around the world was used to generate hundreds of thousands of fold predictions for each design sequence. These results were then compiled into an "energy landscape" for each design sequence. For symmetric multi-chain designs, additional docking simulations were executed to sample alternative inter-molecular interactions. Only designs which show strong preference for the intended fold and docking scheme are included below.

In some cases, the prediction results suggested that a design could be significantly improved with minimal modification. Some of the designs to be tested are slightly modified versions of the player designs shown below. Please note that many solutions from past Foldit puzzles are still being processed.


SimplySue
tokens
MurloW
Anthropic Dreams, Puzzle 789


bruno.kestemont
smilingone
bertro
Beta Folders, Puzzle 789


gitwut
dembones
Contenders, Puzzle 789


Museka
L'Alliance Francophone, Puzzle 789


Ashrai
frood66
Gargleblasters, Puzzle 735


johnmitch
Puzzle 735


Galaxie
auntdeen
Anthropic Dreams, Puzzle 720


Galaxie
jamiexq
tokens
Anthropic Dreams, Puzzle 742


Museka
L'Alliance Francophone, Puzzle 742


Grom
Russian Team, Puzzle 764


pauldunn
gloverd
Go Science, Puzzle 764

( Posted by  bkoep 81 1151  |  Fri, 11/01/2013 - 06:28  |  2 comments )
6
wisky's picture
User offline. Last seen 7 weeks 2 days ago. Offline
Joined: 07/13/2011
Very nice!

Love all of these, they look so beautiful. Congrats guys!

Joined: 09/24/2012
Groups: Go Science
Very exciting

and a motivate to continue folding !

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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, Microsoft, Adobe, RosettaCommons