David Levitt, Principal Investigator

Development of Software for Automated Fitting of X-ray Crystallographic Electron Density Maps

There have been huge technical advances in recent years in the solution of protein structures by x-ray crystallography. The combination of synchrotron xray sources and selenomethione multi-wavelength anomalous dispersion (SMAD) phasing techniques made the generation of high-resolution electron density maps a routine procedure; the researchers began developing a program to automate this. The goal was to submit the electron density map and the amino acid sequence to the computer, which then returns an accurate initial structure that can be used as input to refinement programs. These researchers found they were able to automatically fit nearly all secondary structures. The next step was to extend secondary structures into the loop regions.

The researchers also performed routine refinement of x-ray crystallographic protein structures using either xplor and ncs. Testing was undertaken for a new software package under development; this attempted to automate the fitting of electron density maps. It should be possible to assign the amino acid residues, complete the loops, and refine the side chain atom positions.

The development of these programs required extensive time on a graphics workstation. Each step in the fitting process was monitored using a protein visualization program developed specifically for this project. In addition, a large number of procedures required optimization. The most direct way was to run the program many times with different parameter sets and find the set that gives the best fit to the density. This optimization was performed on the Origin 2000.

Research Group

Mariah B. Olson, Supercomputing Institute Undergraduate Intern