[P2P-F] Fwd: On-line gamers succeed where scientists fail - predicting the structure of protein molecules

[Michel Bauwens]

---------- Forwarded message ----------
From: Dante-Gabryell Monson <dante.monson at gmail.com>
Date: Fri, Sep 23, 2011 at 6:29 PM
Subject: On-line gamers succeed where scientists fail - predicting the
structure of protein molecules
To: econowmix at googlegroups.com


http://www.kurzweilai.net/on-line-gamers-succeed-where-scientists-fail-opening-door-to-new-aids-drug-design

Online gamers have solved the structure of a retrovirus enzyme whose
configuration had stymied scientists, biochemist Firas Khatib of the University
of Washington <http://www.washington.edu/> (UW)
reports<http://nsf.gov/news/news_summ.jsp?cntn_id=121680&org=NSF&from=news>
.

The players were adept at a computer game, Foldit, that allows players to
collaborate and compete in predicting the structure of protein molecules.

---------- Forwarded message ----------
From: R
Date: Wed, Sep 21, 2011 at 10:07 PM
Subject: On-line gamers succeed where scientists fail, opening door to new
AIDS drug design
To:


[image: Fold It]<http://www.kurzweilai.net/on-line-gamers-succeed-where-scientists-fail-opening-door-to-new-aids-drug-design/fold-it>

The "unsolved monkey virus protein" Foldit puzzle, highlighting the tool
used by online gamers (credit: University of Washington)

Online gamers have solved the structure of a retrovirus enzyme whose
configuration had stymied scientists, biochemist Firas Khatib of the University
of Washington <http://www.washington.edu/> (UW)
reports<http://nsf.gov/news/news_summ.jsp?cntn_id=121680&org=NSF&from=news>
.

The players were adept at a computer game, Foldit, that allows players to
collaborate and compete in predicting the structure of protein molecules.

After scientists repeatedly failed to piece together the structure of a
protein-cutting enzyme from an AIDS-like virus, they called in the Foldit
players and challenged them to produce an accurate model of the enzyme.

Remarkably, the gamers generated models good enough for the researchers to
refine and determine the enzyme’s structure within a few days. Equally
amazing, surfaces on the molecule stood out as likely targets for drugs to
deactivate the enzyme.

This class of enzymes, called retroviral proteases, has a critical role in
how the AIDS virus matures and proliferates. Intensive research is underway
to try to find anti-AIDS drugs that can block these enzymes, but efforts
were hampered by not knowing exactly what the retroviral protease molecule
looked like.

“These features provide exciting opportunities for the design of retroviral
drugs, including AIDS drugs,” write Khatib and co-authors (including the
gamers) of a paper appearing yesterday in the journal *Nature Structural &
Molecular Biology*.

“Online gamers have solved a longstanding scientific problem, perhaps
leading the way to new anti-viral drugs,” said Carter Kimsey, program
director in the National Science Foundation’s (NSF) Division of Biological
Infrastructure, which funded the research.

Fold-it was created by computer scientists and biochemists at the UW Center
for Game Science, and by paper co-author biochemist David Baker of UW, to
engage the general public in scientific discovery.

The solution of the virus enzyme structure, the scientists said, indicates
the power of online computer games to channel human intuition and of
three-dimensional pattern-matching skills to solve challenging scientific
problems. The online protein folding game captivates thousands of avid
players worldwide.

Direct manipulation tools, as well as assistance from a computer program
called Rosetta, encourage participants to configure graphics into a workable
protein model. Teams send in their answers, and UW researchers constantly
improve the design of the game and its puzzles by analyzing the players’
problem-solving strategies.

Figuring out the shape and misshape of proteins contributes to research on
causes of and cures for cancer, Alzheimer’s, immune deficiencies, and a host
of other disorders, as well as to environmental work on biofuels.

Games like Foldit are evolving. To piece together the retrovirus enzyme
structure, Cooper said, Foldit used a new alignment tool for the first time
to copy parts of known molecules and test their fit in an incomplete model.

“The ingenuity of game players,” the paper concludes, “is a formidable force
that, if properly directed, can be used to solve a wide range of scientific
problems.”

Ref.: Firas Khatib, et al., Crystal structure of a monomeric retroviral
protease solved by protein folding game players, *Nature Structural and
Molecular Biology*, 2011;
[DOI:10.1038/nsmb.2119<http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.2119.html>
]

Read full article
here...<http://www.kurzweilai.net/on-line-gamers-succeed-where-scientists-fail-opening-door-to-new-aids-drug-design>

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