Walter Chazin

Biomolecular structure determination using crystallographic, spectroscopic, and purely computational approaches

There is a vast untapped potential within the context of understanding biomacromolecular structure that can be explored with the availability of a parallel computer. The ability to search the conformational space available to biomacromolecules such as proteins, RNA and DNA by computational methods such as molecular dynamics simulations is invaluable for the determination of three-dimensional structures. Simplified versions of the full searches are currently used for the refinement of high-resolution structures derived from NMR and X-ray crystallographic data, largely because of the insufficiency of the available compute power.

A parallel system is uniquely well-suited to this problem, because each processor can be used to perform the requisite calculations for an atom or subset of atoms, thereby increasing the effective throughput and yielding a vast increase in the speed at which such simulations can be completed. This large increase in speed opens up completely new horizons in the area of full conformational searches and especially in ab-initio protein folding calculations (i.e., protein structure predictions from sequence). These approaches are essential to the structural genomics revolution, which will require at least an order of magnitude increase in the rate at which three-dimensional structures will be determined. The techniques to be utilized have already been implemented on standard commercial UNIX-based systems and the increased power of doing so is clearly demonstrated.

Links:
Professor Walter Chazin's page
Center for Structural Biology