Sphericity of a protein via the β-complex

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Title
Sphericity of a protein via the β-complex
Author(s)
D S Kim; J K Kim; C I Won; C M Kim; J Y Park; Jong Hwa Park
Bibliographic Citation
Journal of Molecular Graphics & Modelling, vol. 28, no. 7, pp. 636-649
Publication Year
2010
Abstract
Molecular shape is a fundamental factor in determining the function of a molecule. As proteins tend to fold into globular shapes, the shape descriptor for protein sphericity is important in understanding molecular functions. In this paper, a definition of protein sphericity is introduced based on the recently developed geometric constructs of the β-complex and β-shape of a protein. The β-complex represents the Euclidean proximity among all the atoms in a protein, and the β-shape is the polyhedron contained within the boundary of the corresponding β-complex. Hence, the β-shape determines the proximity among the atoms on the boundary of a protein. Given the volume of a β-shape, the ratio between the surface area of a sphere with this volume and the surface area of the β-shape itself is a good measure to classify the sphericity of a protein, especially when the radius of a probe is 3.0 A. The presented measure is invariant to translation and rotation.
Keyword
β-complexβ-shapePDBProtein structureSphericityVoronoi diagram
ISSN
1093-3263
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.jmgm.2010.01.001
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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