Three-dimensional alpha shapes
ACM Transactions on Graphics (TOG)
On the definition and the construction of pockets in macromolecules
Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
Cutting and Stitching: Converting Sets of Polygons to Manifold Surfaces
IEEE Transactions on Visualization and Computer Graphics
Nonmanifold Topology Based on Coupling Entities
IEEE Computer Graphics and Applications
Vertex-based boundary representation of nonmanifold geometric models
Vertex-based boundary representation of nonmanifold geometric models
An efficient algorithm for three-dimensional β-complex and β-shape via a quasi-triangulation
Proceedings of the 2007 ACM symposium on Solid and physical modeling
Molecular surfaces on proteins via beta shapes
Computer-Aided Design
Computer-Aided Design
Manifoldization of β-shapes in O(n) time
Computer-Aided Design
Protein-ligand docking based on beta-shape
Transactions on computational science IX
Protein-ligand docking based on beta-shape
Transactions on computational science IX
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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.