Application of core trace algorithm for determination of protein backbone.

摘要

Protein crystallography is one of the most important methods for determining protein structure. However, building the protein structure from the crystallographic data is often a long and difficult process. The critical point analysis is an automatic system to completely interpret the protein electron density map. The analysis represents the crystallographic data as a critical point graph. This graph contains paths which trace the backbone and side chain of the proteins.; The most important part in the critical point analysis is the determination of the critical points in the map. It depends on the creation of a continuous electron density function which specifies the electron density for any point in the map. However, evaluating such a function is difficult because many parameters are needed. This thesis determines the critical points in the map by using the core trace algorithm. It also develops a system to identify the protein backbone from the critical points. The system was tested on both experimental and ideal electron density map. In most of the proteins, more than 80% of the residues in the protein backbone were correctly identified.