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On the definition and the construction of pockets in macromolecules
H Edelsbrunner1, M Facello, J Liang
1Department of Computer Science, University of Illinois at Urbana-Champaign, USA.
Abstract:
The shape of a protein is important for its functions. This includes the location and size of identifiable regions in its complement space. We formally define pockets as regions in the complement with limited accessibility from the outside. Pockets can be efficiently constructed by an algorithm based on alpha complexes. The algorithm is implemented and applied to proteins with known three-dimensional conformations.