HP 1/10GB Virtual Connect Ethernet Module for c-Class BladeSystem 399593-B22#0D1 产品宣传页
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If researchers can find the right compound—one that
inhibits the replication of any of these viruses—it could
be used to treat viral infections and improve, extend,
or even save those lives.
inhibits the replication of any of these viruses—it could
be used to treat viral infections and improve, extend,
or even save those lives.
This race is underway at many locations. One of them
is Princeton, New Jersey, at a company called
Pharmasset, Inc. One of the many levels of research
work taking place there happens not in a lab, but
inside a number of high-powered silicon chips in the
company’s server room—on four server blades in an
enclosure about the size of a small dormitory
refrigerator.
is Princeton, New Jersey, at a company called
Pharmasset, Inc. One of the many levels of research
work taking place there happens not in a lab, but
inside a number of high-powered silicon chips in the
company’s server room—on four server blades in an
enclosure about the size of a small dormitory
refrigerator.
How to thwart a deadly virus
Pharmasset’s head of computational chemistry, Ralph
Mosley, uses those server blades to perform molecular
docking with the goal of identifying potential inhibitors
of viral replication—a type of test that could be
performed by Pharmasset’s biologists in a real lab with
pipettes and 96-well assay plates. But, by simulating
the tests on a server, Mosley can run them much faster.
This saves time and effort for the experimentalists by
allowing them to focus on the compounds most likely to
be effective inhibitors. Aside from docking existing
compounds, Mosley can put virtual molecules together
that look similar to components of DNA or RNA in
ways that haven’t occurred in nature yet. Either
approach could lead to the good news that millions of
people are hoping for.
Pharmasset’s head of computational chemistry, Ralph
Mosley, uses those server blades to perform molecular
docking with the goal of identifying potential inhibitors
of viral replication—a type of test that could be
performed by Pharmasset’s biologists in a real lab with
pipettes and 96-well assay plates. But, by simulating
the tests on a server, Mosley can run them much faster.
This saves time and effort for the experimentalists by
allowing them to focus on the compounds most likely to
be effective inhibitors. Aside from docking existing
compounds, Mosley can put virtual molecules together
that look similar to components of DNA or RNA in
ways that haven’t occurred in nature yet. Either
approach could lead to the good news that millions of
people are hoping for.
“There are about 350,000 molecules in our database,
all of which have to go into a binding cavity and a
protein in our simulation,” Mosley explains. “There are
usually different conformations for each molecule
being tested, if you will, in a binding cavity. So we
need to be able to run up to between five to ten million
simulations over 18 hours or so.”
all of which have to go into a binding cavity and a
protein in our simulation,” Mosley explains. “There are
usually different conformations for each molecule
being tested, if you will, in a binding cavity. So we
need to be able to run up to between five to ten million
simulations over 18 hours or so.”
Mosley and other researchers then analyze the
simulation results to search for promising leads. Those
leads will be further explored by researchers in the
company’s actual physical labs.
simulation results to search for promising leads. Those
leads will be further explored by researchers in the
company’s actual physical labs.
It comes down to this
How fast can the simulations be run? And how fast
can the servers and simulation software needed to run
them be deployed? These are two critical factors in this
race, and it fell to Jim Anuth, Director of Information
Technology at Pharmasset, to come up with the most
appropriate computing solution. Every day,
Pharmasset’s competitors are racing to find the right
combination first.
How fast can the simulations be run? And how fast
can the servers and simulation software needed to run
them be deployed? These are two critical factors in this
race, and it fell to Jim Anuth, Director of Information
Technology at Pharmasset, to come up with the most
appropriate computing solution. Every day,
Pharmasset’s competitors are racing to find the right
combination first.
“Other companies big and small are conducting this
high throughput screening in computational chemistry,”
Mosley explains. “Based on how these tiny molecular
fragments sit inside of a binding cavity, they can be
connected together to make a completely novel drug.”
high throughput screening in computational chemistry,”
Mosley explains. “Based on how these tiny molecular
fragments sit inside of a binding cavity, they can be
connected together to make a completely novel drug.”
If a drug is unique and can be patented, Anuth points
out, “as it improves millions of lives, it could also be a
billion-dollar product.”
out, “as it improves millions of lives, it could also be a
billion-dollar product.”
Which computing solution is right?
Pharmasset had just a 600-square foot server room
and 45 people on staff in fall 2007 when Mosley
joined. There were less than two racks of server space
left, and the one-person IT staff was Jim Anuth. Another
IT person has joined him on the team since.
Pharmasset had just a 600-square foot server room
and 45 people on staff in fall 2007 when Mosley
joined. There were less than two racks of server space
left, and the one-person IT staff was Jim Anuth. Another
IT person has joined him on the team since.
“With the savings in software licensing
alone, the HP solution paid for itself.”
Jim Anuth, Director of Information Technology,
Pharmasset
alone, the HP solution paid for itself.”
Jim Anuth, Director of Information Technology,
Pharmasset