Computation of protein geometry and its applications: Packing and function prediction

Details Computation of protein geometry and its applications: Packing and function prediction Computation of protein geometry and its applications: Packing and function prediction

2006-01-14

arxiv.org/abs/q-bio/0601020v1

Biology

Quantitative Biology

Biomolecules

32 pages, 9 figures

Scientific paper

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.

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