Forum 12/04/2008

“Fast Automated Reconstruction of Icosahedral Viruses from Cryo-electron Micrographs”

Robert Sinkovits, Ph.D. – San Diego Supercomputer Center, UCSD, La Jolla, CA

Cryo-electron microscopy is the technique of choice for solving the structures of biological macromolecules that resist crystallization. Although many of the individual steps in a full structure determination project can be quite involved, the image reconstruction process is often rate limiting. In an effort to minimize the time, effort, and computer savvy needed to generate 3D structures from cryo-electron micrographs, we have developed AUTO3DEM, a fast, automated image reconstruction system for icosahedral viruses. All of the underlying numerically intensive applications have been carefully tuned to achieve optimal performance and parallelized using the Message Passing Interface (MPI) library. In the best cases, computations that had formerly taken many months to complete can now be finished in a matter of hours once boxed image data is available. An overview of the software and its capabilities will be provided together with some recent results. I will also discuss our plans to extend AUTO3DEM to particles without icosahedral symmetry and to perform image reconstructions in near real-time directly at the microscope.