[ILUG] OT: Folding@Home Yields Results Published in Nature (fwd)

[Justin Mason]

just in time!  I hope this isn't what kicked off the talk of all these
screensavers...

--j.

------- Forwarded Message

Date:    Tue, 22 Oct 2002 09:58:44 -0700
From:    "Gordon Mohr" <gojomo at usa.net>
To:      <fork at xent.com>
Subject: Folding at Home Yields Results Published in Nature

  Folding at home scientists report first distributed computing success
  http://www.stanford.edu/dept/news/pr/02/folding1023.html

Congrats to Adam Beberg and Cosm, creditted as key enablers of 
Folding at Home:

  http://folding.stanford.edu/about.html


# 10/21/02
# 
# Mark Shwartz, News Service: (650) 723-9296, mshwartz at stanford.edu
# 
# EDITORS: The Nature study, "Absolute comparison of simulated and
# experimental protein-folding dynamics," is available online at
# www.nature.com. A photograph of Stanford Assistant Professor Vijay
# Pande can be downloaded at http://newsphotos.stanford.edu (slug:
# "Pande").
# 
# Relevant Web URLs:
# http://folding.stanford.edu
# http://www.stanford.edu/group/pandegroup/
# http://www.research.ibm.com/bluegene/
# 
# 
# Folding at home scientists report first distributed computing success
# 
# As you read this sentence, millions of personal computers around the
# world are working overtime -- performing complex computations on their
# screensavers in the name of science. This growing Internet phenomenon,
# known as "distributed computing," is being used for everything from
# the search for extraterrestrial intelligence to the design of new
# therapeutic drugs.
# 
# Now, for the first time, a distributed computing experiment has
# produced significant results that have been published in a scientific
# journal. Writing in the advanced online edition of Nature magazine,
# Stanford University scientists Christopher D. Snow and Vijay S. Pande
# describe how they -- with the help of 30,000 personal computers --
# successfully simulated part of the complex folding process that a
# typical protein molecule undergoes to achieve its unique, three-
# dimensional shape. Their findings were confirmed in the laboratory of
# Houbi Nguyen and Martin Gruebele, scientists from the University of
# Illinois at Urbana-Champaign who co-authored the Nature study.
# 
# Understanding disease
# 
# Every protein molecule consists of a chain of amino acids that must
# assume a specific three-dimensional shape to function normally.
# 
# "The process of protein folding remains a mystery," said Pande,
# assistant professor of chemistry and of structural biology at
# Stanford. "When proteins misfold, they sometimes clump together,
# forming aggregates in the brain that have been observed in patients
# with Alzheimer's, Parkinson's and other diseases."
# 
# How proteins fold into their ideal conformation is a question that has
# tantalized scientists for decades. To solve the problem, researchers
# have turned to computer simulation -- a process that requires an
# enormous amount of computing power.
# 
# "One reason that protein folding is so difficult to simulate is that
# it occurs amazingly fast," Pande explained. "Small proteins have been
# shown to fold in a timescale of microseconds [millionths of a second],
# but it takes the average computer one day just to do a one-nanosecond
# [billionth-of-a-second] folding simulation."
# 
# Simulating protein folding is often considered a "holy grail" of
# computational biology, he added. "This is an area of hot competition
# that includes a number of heavyweights, such as IBM's $100 million,
# million-processor Blue Gene supercomputer project."
# 
# Folding at home
# 
# Two years ago, Pande launched Folding at home -- a distributed computing
# project that so far has enlisted the aid of more than 200,000 PC
# owners, whose screensavers are dedicated to simulating the protein-
# folding process.
# 
# The Stanford project operates on principles similar to earlier
# projects, such as SETI at home, which allows anyone with an Internet
# connection to search for intelligent life in the universe by
# downloading special data-analysis software. When a SETI at home
# screensaver is activated, the PC begins processing packets of radio
# telescope data. Completed packets are sent back to a central computer,
# and new ones are assigned automatically.
# 
# For the Nature study, Pande and Snow, a biophysics graduate student,
# asked volunteer PCs to resolve the folding dynamics of two mutant
# forms of a tiny protein called BBA5. Each computer was assigned a
# specific simulation pattern based on its speed.
# 
# With 30,000 computers at their disposal, Pande and Snow were able to
# perform 32,500 folding simulations and accumulate 700 microseconds of
# folding data. These simulations tested the folding rate of the protein
# on a 5-, 10- and 20-nanosecond timescale under different temperatures.
# Using these data, the scientists were able to predict the folding rate
# and trajectory of the "average" molecule.
# 
# Experimental verification
# 
# To confirm their predictions, the Stanford team asked Gruebele and
# Nguyen to conduct "laser temperature-jump experiments" at their
# Illinois lab. In this technique, an unfolded protein is pulsed with a
# laser, which heats the molecule just enough to cause it to bend into
# its native state. A fluorescent amino acid imbedded inside the
# molecule grows dimmer as the protein folds. Researchers use the
# changing fluorescence to measure folding events as they occur.
# 
# The results of the laser experiments were in "excellent agreement"
# with the Folding at home predictions, Pande and his colleagues concluded.
# Specifically, the computers predicted that one experimental protein
# would fold in 6 microseconds, while laboratory observations revealed
# an actual folding time of 7.5 microseconds.
# 
# "These experiments represent a great success for distributed
# computing," Pande said. "Understanding how proteins fold will likely
# have a great impact on understanding a wide range of diseases."
# 
# The Nature study was supported by the National Institutes of Health,
# the American Chemical Society, Intel and the Howard Hughes Medical
# Institute.
# 
# 
# 
# Caroline Uhlik is a science writing intern at Stanford News Service.
# 
# -30-
# 
# By Caroline Uhlik and Mark Shwartz




- Gordon



------- End of Forwarded Message