About the Lab

D. E. Shaw Research ("DESRES") is an independent research laboratory that conducts basic scientific research in the field of computational biochemistry under the direct scientific leadership of Dr. David Shaw, who serves as its Chief Scientist. At present, the lab is involved primarily in

• The design of novel algorithms and machine architectures for high-speed molecular dynamics (MD) simulations of proteins and other biological macromolecules

• The application of such simulations to basic scientific research in structural biology and biochemistry, and to the process of computer-aided drug design

Members of the lab include computational chemists and biologists, computer scientists and applied mathematicians, and computer architects and engineers, all working collaboratively within a tightly coupled interdisciplinary research environment.

Current projects include

• The extension and enhancement of Desmond, an MD code developed within our lab that uses novel parallel algorithms and numerical techniques to achieve very high performance on a conventional commodity cluster. We are making Desmond available without cost for non-commercial use at universities and other not-for-profit research institutions. While our lab is not itself engaged in the marketing of software to commercial firms, a commercial version of Desmond is expected to be marketed by Schrödinger, LLC later this year.

• The implementation and deployment of Anton, a specialized, massively parallel supercomputer designed to execute MD simulations hundreds of times faster than has been possible to date. When it becomes operational (around the end of 2008, according to our current projections), we are hopeful that Anton will allow scientists to observe, for example, the structural changes in proteins that underlie important biological phenomena occurring on time scales far in excess of those that have thus far been computationally accessible.

• The development of computational chemistry methods to enable more accurate and effective MD simulations. Our efforts in this area include the creation of improved molecular mechanics force fields, the comparison of simulation results to experimental measurements, and the exploratory development of novel methods for efficiently sampling the conformational space of proteins and other biomolecules.

• The application of MD simulations to elucidate the functional dynamics of proteins at an atomic level of detail. We are investigating, for example, the mechanisms of several membrane transport proteins, and of certain protein kinases that play a critical role in the development and treatment of cancer. In the course of such research, we have entered into collaborative relationships with several experimental laboratories to help us better understand specific biological systems and to validate predictions that we have made based on our analyses of simulation data.