I tweeted out a drawing from when I was
eight years old where it was my biggest
daydream it's a picture of a big
computer and says I want to have the
biggest computer in the world
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yeah you know with Foley at home is that
we want to perform simulations of
protein dynamics proteins are the
molecular machines that perform lots of
the processes that we associate with
life everything for a muscle contraction
- structural roles like your hair and
catalyzing chemical reactions and so we
really want to understand all of these
moving parts but there's no experimental
means to watch these proteins in action
as a decide that were talking about and
so our approach is to simulate them in a
computer and the reason that bowling at
home exists of these calculations are
extremely computationally expensive so
even our easy problems you have take
like a hundred years on a typical
desktop computer so what we've done is
developed out rows where we can split
these enormous calculations up into lots
of small chunks that can be performed in
parallel independent of one another and
then ask people around the world to
volunteer to run these chunks of
simulations on their personal computers
boards you don't have to have a really
fast computer to participate in all day
at home we can make use of everything
people can give us
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holding at home is estimated to be by
far the largest supercomputer in the
world by one back the envelope
calculation we have more compute power
than the top 100 supercomputers combined
and we're throwing as much of this as we
can at Kovac 19 and trying everything we
can in parallel
the end of February we had about 30,000
active volunteers in the past three
weeks though we've had over 700,000
people joined the project so the idea is
that experimentally we can see a
snapshot of what many of these proteins
usually look like but that still leaves
us blind to lots of the moving parts
that are important for their functions
this is if you're trying to understand a
football game but all you can see is
what the players usually look like which
is them lined up at the line of
scrimmage so there's information there
but really you want to see the rest of
the game as the process unfolds and so
that's what we're able to do with our
simulations so so just to give one
example we've been looking at a protein
complex actually called the spike
there's many copies of this that
decorate the surface of the virus as
actually consists of three proteins that
kind of come together and in order to
infect a human cell the end of this has
to open up to reveal the interface that
actually binds to a human cell and
initiates infection and so we'd like to
see this process occur and actually see
what the open state looks like with the
atomic detail that we need to start
doing things like designing therapeutics
to target different structures along
this whole range of motion and it does
really go like this so so it kind of
reminded us of one of the Devon Gorgon
monsters from the television series
strange of things so we we've taken to
calling it the kovat 19th and the cork
it doesn't have to so so when you
install the software you can tell us
what fraction of your computer you we
can use you can also set things with a
software only runs where your computer
has been idle for a certain amount of
time so we're not using it all when you
want to use a condition so this is a
specific protein called beta lactamase
it's involved in antibiotic resistant
bacteria express it because it's really
good at in activating penicillin and
related antibiotics and what we can see
about 23 seconds in is the spontaneous
opening of this deep groove that we call
a cryptic pocket because it's absent in
that a starting structure where there's
no groove we've shown that this provides
us with a novel handle to design small
molecules to shut down the function of
this protein you know I think one of the
really exciting things about this is to
see people really banding together to
rally around a common goal and one of
the things that we have to offer people
as the legitimate opportunity to be part
of trying to tackle this pandemic
washing your hands and social distancing
and all of this are extremely important
but I think it's still gratifying to
feel like you can proactively do
something to deal with this crisis
you
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