Characterizing oriented protein structural sites using biochemical properties.

Reference: Bagley, S. C.; Wei, L.; Cheng, C.; & Altman, R. B. Characterizing oriented protein structural sites using biochemical properties. Knowledge Systems Laboratory, Medical Computer Science, March, 1995.

Abstract: A protein site is a region of a three-dimensional protein structure, with a distinguishing functional or structural role. Certain sites recur in different protein structures (for example catalytic sites, calcium binding sites, and some types of turns), but maintain critical shared features. To facilitate the analysis of such protein sites, we have developed a system for analyzing the spatial distributions of biochemical properties around a site. Simply put, the system takes a set of similar sites and a set of control nonsites, and finds differences between them. Specifically, it compares distributions of the properties surrounding the sites with those surrounding the nonsites, and reports significant differences. In this paper, we apply our method to analysis of the features of the active site of the serine protease enzymes. We compare the use of radial distributions (shells) with 3-D grids (blocks) in the analysis of the active site. We demonstrate three different strategies for focusing attention on significant findings, based on properties of interest, spatial volumes of interest, and on the level of statistical significance. Finally, we show that the program automatically identifies conserved sequential, secondary structural and biophysical features of the serine protease active site, using noncatalytic histidine residues as a control environment.

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