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JISC-VRE  May 2008

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Subject:

FYI: [CAnet - news] Researchers Launch Online Protein Folding Game

From:

Frederique van Till <[log in to unmask]>

Reply-To:

Frederique van Till <[log in to unmask]>

Date:

Mon, 12 May 2008 17:01:59 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (125 lines)

For more information on this item please visit my blog at

http://green-broadband.blogspot.com/ or http://billstarnaud.blogspot.com
-------------------------------------------


[Another great example of the potential of Citizen Science. Extracts from
Slashdot and original article--BSA

Researchers Launch Online Protein Folding Game
http://www.hhmi.org/news/foldit20080508.html

Multiplayer online gaming brings to mind fabulously successful titles, such
as "World of Warcraft" and "Ultima." On May 8, Howard Hughes Medical
Institute (HHMI) researchers at the University of Washington are bringing
the arcane world of protein folding to the online gaming arena with the
launch of "Foldit," a free game in which players around the world compete to
design proteins. The real world benefit: Scientists will test proteins
designed by the game's players to see if they make viable candidate
compounds for new drugs.

Users can access the game via the web at www.fold.it

The development of the online game is a natural extension of HHMI
investigator David Baker's quest to understand how proteins - the building
blocks of cells - fold into unique three-dimensional shapes. Over the past
decade, Baker and his colleagues have made steady progress in developing
computer algorithms to predict how a linear string of amino acids will fold
into a given protein's characteristic shape. A detailed understanding of a
protein's structure can offer scientists a wealth of information - revealing
intricacies about the protein's biological function and suggesting new ideas
for drug design.

Predicting the shapes that natural proteins will take is one of the
preeminent challenges in biology, and modeling even a small protein requires
making trillions of calculations. Over the last three years, volunteers
around the globe - now numbering about 200,000- have donated their computer
down-time to performing those calculations in a distributed network called
[log in to unmask] The computing logic behind the network is an algorithm called
Rosetta that uses the Monte Carlo technique to find the best "fit" for all
of the parts of a given protein.

But as the Rosetta volunteers watched their computers blindly trying to work
out a solution by methodically testing every possible combination and shape
to find the best fit, they began to think that a little human intervention
might speed things up. "People were writing in, saying, `Hey! The computer
is doing silly things! It would be great if we could help guide it,'"
remembers Baker, who is based at the University of Washington (UW) where he
developed the Rosetta algorithm and network.

Baker didn't know how he could make that happen until about 18 months ago,
when he went hiking on Mt. Rainier with his neighbor David Salesin, a
University of Washington computer scientist who also runs a research
laboratory at nearby Adobe Systems. Baker and Salesin began discussing ways
to make Rosetta more interactive. With the inherent fun of competition,
Salesin thought a multiplayer online game was the way to go. By the time
they got back to the car, they had settled on that idea. Salesin provided
Baker with the names of three colleagues, led by UW computer scientist Zoran
PopoviŠ, who could help Baker create the game.

Over the next several months, PopoviŠ, and his students Adrien Treuille and
Seth Cooper, created the program, and the team tested it in small venues.
One match between teams from the University of California and the University
of Illinois aroused unexpected fervor and cheering among spectators. "30 or
40 people participated," says Baker. "The competition was very intense."

"Foldit" takes players through a series of practice levels designed to teach
the basics of protein folding, before turning them loose on real proteins
from nature. "Our main goal was to make sure that anyone could do it, even
if they didn't know what biochemistry or protein folding was," says PopoviŠ.
At the moment, the game only uses proteins whose three-dimensional
structures have been solved by researchers. But, says PopoviŠ, "soon we'll
be introducing puzzles for which we don't know the solution."

Baker has high hopes that the game will speed up the sometimes tedious
business of structure prediction. But the part of the game that excites him
most is scheduled to debut this fall, when gamers will be able to design
all-new proteins. Novel proteins could find use in any number of
applications, from pharmaceuticals to industrial chemicals, to pollution
clean up. With the ability for any person with a computer and an internet
hookup to start building proteins, Baker thinks the pace of discovery could
skyrocket. "My dream is that a 12-year-old in Indonesia will turn out to be
a prodigy, and build a cure for HIV," he says.

http://games.slashdot.org/games/08/05/08/2112208.shtml

writes "Tired of justifying your gaming addiction? Now you can really help
accomplish something while you play... thanks to Howard Hughes Medical
Institute researcher David Baker at the University of Washington." In
collaboration with others, Baker has designed a game, called "Foldit," with
a practical outcome: players manipulate on-screen images of protein chains
and attempt to predict their folding patterns. From the article: "'Our main
goal was to make sure that anyone could do it, even if they didn't know what
biochemistry or protein folding was,' says [co-creator Zoran] Popovic. At
the moment, the game only uses proteins whose three-dimensional structures
have been solved by researchers. But, says Popovic, 'soon we'll be
introducing puzzles for which we don't know the solution.'"


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These news items and comments are mine alone and do not necessarily reflect
those of the CANARIE board or management.
-----------
[log in to unmask]
[log in to unmask]
web: www.canarie.ca/~bstarn
skype: pocketpro
blog: http://billstarnaud.blogspot.com/


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