Characterizing the Microenvironment Surrounding Protein Sites

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Citation: Steven C. Bagley and Russ B. Altman. (1994) Characterizing the Microenvironment Surrounding Protein Sites. In KSL-94-72, November,1994.

Publication techreport ( Edit )
type Technical Report
bibtype techreport
Bibtex basics
author Steven C. Bagley and Russ B. Altman
title Characterizing the Microenvironment Surrounding Protein Sites
number KSL-94-72
institution Knowledge Systems, AI Laboratory
year 1994
month November
Bibtex more
note Updated May 1995.
Access Paper
abstract Sites are microenvironments within a biomolecular structure, distinguished by their structural or functional role. A site can be defined by a three-dimensional location, and a local neighborhood around this location in which the structure or function exists. We have developed a system to facilitate structural analysis (both qualitative and quantitative) of biomolecular sites. Our system automatically examines the spatial distributions of biophysical and biochemical properties, and reports those regions within a site where the distribution of these properties differs significantly from control nonsites. The properties range from simple atom-based characteristics such as charge to polypeptide-based characteristics such as type of secondary structure. Our analysis of sites uses nonsites as controls, providing a baseline for the quantitative assessment of the significance of the features that are uncovered. In this paper, we use radial distributions of properties to study three well-known sites (the binding sites for calcium, the milieu of disulfide bridges, and the serine protease active site). We demonstrate that the system automatically finds many of the previously described features of these sites, and augments these features with some new details. In some cases,we can not confirm the statistical significance of previously reported features. Our results demonstrate that analysis of protein structure is sensitive to assumptions about background distributions, and that these distributions should be considered explicitly during structural analyses.

KSL Technical Report ID: KSL-94-72
Facts about Characterizing the Microenvironment Surrounding Protein SitesRDF feed
Abstract Sites are microenvironments within a biomo … Sites are microenvironments within a biomolecular structure, distinguished by their structural or functional role. A site can be defined by a three-dimensional location, and a local neighborhood around this location in which the structure or function exists. We have developed a system to facilitate structural analysis (both qualitative and quantitative) of biomolecular sites. Our system automatically examines the spatial distributions of biophysical and biochemical properties, and reports those regions within a site where the distribution of these properties differs significantly from control nonsites. The properties range from simple atom-based characteristics such as charge to polypeptide-based characteristics such as type of secondary structure. Our analysis of sites uses nonsites as controls, providing a baseline for the quantitative assessment of the significance of the features that are uncovered. In this paper, we use radial distributions of properties to study three well-known sites (the binding sites for calcium, the milieu of disulfide bridges, and the serine protease active site). We demonstrate that the system automatically finds many of the previously described features of these sites, and augments these features with some new details. In some cases,we can not confirm the statistical significance of previously reported features. Our results demonstrate that analysis of protein structure is sensitive to assumptions about background distributions, and that these distributions should be considered explicitly during structural analyses. red explicitly during structural analyses.
Author Steven C. Bagley and Russ B. Altman  +
Bibtype techreport  +
Has author Steven C. Bagley and Russ B. Altman  +
Has identifier KSL-94-72  +
Has publishing details November,1994  +
Has title Characterizing the Microenvironment Surrounding Protein Sites  +
Has where published KSL-94-72  +
Has year 1994  +
Institution Knowledge Systems, AI Laboratory  +
Ksl tr id KSL-94-72  +
Month November  +
Note Updated May 1995.
Number KSL-94-72  +
Process note YES  +
Title Characterizing the Microenvironment Surrounding Protein Sites  +
Year 1994  +
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