Protein Shell::Core::Face Comparison Server

INTERPARE   The Protein Interfaceome Database

3. Voronoi Diagram





The Voronoi diagram, known as Dirichlet tessellation, has been widely used in the fields of science and engineering. The Voronoi diagram was first introduced as an application to the study of protein structure by Richards et al. (1974, 1977).

There is a report on defining molecular interfaces by Power Diagram - Voronoi Diagram on weighted points set (Varshney et al., 1995). We used the same protocol suggested by Varshney et al., except for two aspects.

First, we did not use polygon filtering by distance threshold in that we already had interfaces defined by distance threshold method.
Second, we calculated interfaces on domains instead of calculating them on protein complexes. We first constructed a three dimensional power-diagram P of the atoms. The construction of such a power diagram will have a time complexity of (n is number of atoms in the protein) where the number of neighbors for any given atom is bounded by a constant.

Each face of the power-diagram P is defined by two atoms (Figure 3).
For each face in P, if two atoms defining a face belong to different domains from each other, we call such face as interface face.
Let us define interface-cell as a cell in the power-diagram P that has at least one interface-face.
Let us define interface-atoms to be those atoms whose cells are interface-cells.

In the InterPare database, all the interface-atoms between two domain pairs are stored in a PDB-style file format. The default van der Waals radii of atoms were taken from Chothia (1976).




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