09-05-2012, 11:17 AM
Global Grid Computing at NYU
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PROTEINS
Proteins are the most important
molecules in living beings. Just about
everything in your body involves
or is made out of proteins. They are
structural molecules made up of long
chains of smaller molecules called
amino acids that act as enzymes
and important carriers of biological
signals. There are 20 amino acids
that combine in different ways to
make up proteins. As the chain of
amino acids is built, the chain folds
(like balling up string) into a more
compact mass, ending up in a particular
shape. This process is called
“protein folding.” Many of the
things that happen in cells are specifically
controlled by protein shapes
and the functions conferred by those
shapes. For example, a protein in a
virus or bacterium may have a particular
shape that interacts with human
proteins or human cell membrane,
enabling it to infect cells. This is an
oversimplification, but nevertheless,
knowing these shapes helps us gain
insight into the biology of disease by
understanding protein function.
AN EXPANDING PROTEIN UNIVERSE
In recent years, scientists have
sequenced many genomes, including
the human genome. Between 20,000
and 30,000 genes found in the human
genome encode proteins. The collection
of all the human proteins in
the genome is known as “the human
proteome.”
PROTEIN STRUCTURE PREDICTION
We’ve known for a while that we
can get good enough structure predictions
using Rosetta to predict
function for large numbers of
proteins. For example, as part of my
PhD at the University of Washington
(Baker Lab), I focused on improving
the Rosetta method and then on predicting
the structures of only 500
key proteins.
WORLD COMMUNITY GRID PILOT PROJECT
The World Community Grid was
started by IBM as a public supercomputing
resource; all results are
made public, and research efforts are
carried out on the non-IBM side by
non-prof it entities. In 2004, IBM
was looking for a biological application
they could use to help test their
grid (also with the aim that work on
the Grid would benef it humanity
and help generate positive publicity).
Given the inherent grid-ability of
our project, we were a natural f it
for the World Community Grid.
We proposed the Human Proteome
Folding Project, and were accepted
as the World Community Grid’s
pilot project.