| Abstract
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Sites are microenvironments within a biomo … Sites are microenvironments within a biomolecular structure, distinguishedby their structural or functional role. A site can be defined by athree-dimensional location, and a local neighborhood around this locationin which the structure or function exists. We have developed a system tofacilitate structural analysis (both qualitative and quantitative) ofbiomolecular sites. Our system automatically examines the spatialdistributions of biophysical and biochemical properties, and reports thoseregions within a site where the distribution of these properties differssignificantly from control nonsites. The properties range from simpleatom-based characteristics such as charge to polypeptide-basedcharacteristics such as type of secondary structure. Our analysis of sitesuses nonsites as controls, providing a baseline for the quantitativeassessment of the significance of the features that are uncovered. In thispaper, we use radial distributions of properties to study three well-knownsites (the binding sites for calcium, the milieu of disulfide bridges, andthe serine protease active site). We demonstrate that the systemautomatically finds many of the previously described features of thesesites, and augments these features with some new details. In some cases,we can not confirm the statistical significance of previously reportedfeatures. Our results demonstrate that analysis of protein structure issensitive to assumptions about background distributions, and that thesedistributions should be considered explicitly during structural analyses. red explicitly during structural analyses.
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