Characterizing oriented protein structural sites using biochemical properties

From Tetherless World Wiki

Jump to: navigation, search

Citation: Steven C. Bagley and Liping Wei and Carol Cheng and Russ B. Altman. (1995) Characterizing oriented protein structural sites using biochemical properties. In KSL-95-31, March,1995.

Publication techreport ( Edit )
type Technical Report
bibtype techreport
Bibtex basics
author Steven C. Bagley and Liping Wei and Carol Cheng and Russ B. Altman
title Characterizing oriented protein structural sites using biochemical properties
number KSL-95-31
institution Knowledge Systems, AI Laboratory
address Stanford, CA, USA
year 1995
month March
Bibtex more
note Medical Computer Science
Access Paper
abstract A protein site is a region of a three-dimensional protein structure, with a distinguishing functional or structural role. Certain sites recur indifferent 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) with3-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.

KSL Technical Report ID: KSL-95-31
Facts about Characterizing oriented protein structural sites using biochemical propertiesRDF feed
Abstract A protein site is a region of a three-dime … A protein site is a region of a three-dimensional protein structure, with a distinguishing functional or structural role. Certain sites recur indifferent 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) with3-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. stidine residues as a control environment.
Address Stanford, CA, USA  +
Author Steven C. Bagley and Liping Wei and Carol Cheng and Russ B. Altman  +
Bibtype techreport  +
Has author Steven C. Bagley and Liping Wei and Carol Cheng and Russ B. Altman  +
Has identifier KSL-95-31  +
Has publishing details March,1995  +
Has title Characterizing oriented protein structural sites using biochemical properties  +
Has where published KSL-95-31  +
Has year 1995  +
Institution Knowledge Systems, AI Laboratory  +
Ksl tr id KSL-95-31  +
Month March  +
Note Medical Computer Science
Number KSL-95-31  +
Process note NO  +
Title Characterizing oriented protein structural sites using biochemical properties  +
Year 1995  +
Retrieved from "http://tw.rpi.edu/wiki/Characterizing_oriented_protein_structural_sites_using_biochemical_properties"
Personal tools