Manifoldization of β-shapes by topology operators

Abstract

It is well known that the geometric structure of a protein is an important factor to determine its functions. In particular, the atoms located at the boundary of a protein are more important since various physicochemical reactions happen in the boundary of the protein. The β-shape is a powerful tool for the analysis of atoms located at the boundary since it provides the complete information of the proximity among these atoms. However, β-shapes are difficult to handle and require heavy weight data structures since they form non-manifold structure. In this paper, we propose topology operators for converting a β-shape into a manifold. Once it is converted, compact data structures for representing a manifold are available. In addition, general topology operators used for manifold structures can also be available for various applications. © 2008 Springer-Verlag Berlin Heidelberg.