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Title 

Sphericity of a protein via the β-complex

Authors 

D S KimJ K KimC I WonC M KimJ Y ParkJong Hwa Park

Publisher 

Elsevier

Issue Date 

2010

Citation 

Journal of Molecular Graphics & Modelling, vol. 28, no. 7, pp. 636-649

Keywords 

β-complexβ-shapePDBProtein structureSphericityVoronoi diagram

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.

ISSN 

1093-3263

Link 

http://dx.doi.org/10.1016/j.jmgm.2010.01.001

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2019-05-02


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