Some links to projects I've worked on at D. E. Shaw Research
D. E. Shaw Research does
basic scientific research in computational biochemistry and molecular
dynamics.
David Shaw's 2006 talk at Stanford University's Computer Systems
Colloquium has both
video and
slides
which provide background, context and elaboration for our lab's work.
We have designed and built Anton, a massively parallel machine for
biomolecular simulation. Some papers
describing science done on Anton:
-
How Fast-Folding Proteins Fold (Science, 28 Oct 2011) reports the
results of many long atomic-level molecular dynamics simulations on
Anton, each run for periods ranging between 100 µs and 1 ms of
simulated time, that reveal a a set of common principles underlying the
folding of 12 structurally diverse proteins. The proteins range in size
from 10 to 80 residues, and include members of all three majoral
structural classes (α-helical, β sheet and mixed
α/β). Each protein was simulated near the melting
temperature (so both folding and unfolding events were likely). For
each protein, between one and four simulations were run for long enough
to observe at least 10 folding and 10 unfolding events. In aggregate,
this represents ˜8 ms of simulation with more than 400 folding and
unfolding events. The proteins were all observed to fold close to their
experimentally determined native structures.
-
How Does a Drug Molecule Find Its Target Binding Site?(JACS, 5 May
2011) provides a continuous, atomic-level view of binding process of a
ligand (the cancer drug dasatinib or the kinase inhibitor PP1) to a
protein (Src kinase). In long, unguided simulations on Anton, the
ligand, initially placed at a random location within a box that also
contained the protein, correctly identified its target binding site.
Watch the movie: the ligand is the orange-brown molecule.
-
Atomic-Level Characterization of the Structural Dynamics of Proteins
(Science, 15 Oct 2010) describes results of various record-length
molecular dynamics simulations on Anton, including a millisecond-long
simulation of BPTI (bovine pancreatic trypsin inhibitor) and hundreds of
microseconds of WW domain and villin headpiece, including complete
folding simulations from a fully extended state]
Papers describing Anton:
A side-project that emerged from Anton is a class of "counter-based"
random number generators (CBRNGs), which we will present at SC11.
CBRNGs are fast, stateless functions that are great for modern
multi-core or distributed applications -- the source code is available
for download. It was interesting getting them to work in C, C++0X as
well as OpenCL (on an AMD HD6970) and CUDA (on an NVIDIA GTX580).
Another of our projects is Desmond, a scalable
molecular dynamics (MD) program for commodity clusters (aka
Beowulfs).
We first described the performance of Desmond on a 2005-vintage
Infiniband+Opteron cluster in
Scalable Algorithms for Molecular Dynamics Simulations on Commodity
Clusters, (SuperComputing 2006, Best Paper). We also released a A
tech report with updated performance numbers on a 2008-vintage
Infiniband+Xeon cluster.
I gave a
talk on D. E. Shaw Research's experience with deploying a large
Infiniband cluster at the
2007 OpenFabrics Sonoma Workshop
The D. E. Shaw Research publications page.
More general articles about D. E. Shaw Research:
My home page.