The SURFNET program generates surfaces and void regions between surfaces including the void forming a surface cleft. Thus it can be used to identify surface clefts which may be binding sites. (It also generates surfaces of buried voids such as cavites or just intermolecular voids.)
This program works by increasing a probe radius to some user defined size. Below are two images, the first was obtained with a probe size between 1.4 - 4.0 Å, and represents those surface clefts which may bind small molecules up to approximately 4 Å. The second image was obtained using a probe size of 1.4 - 10.0 Å and thus includes those surface clefts which may bind something as large as a DNA duplex. This program gives you an idea of the shape of a potential ligand.
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Revised: Tuesday, 20-Oct-1998 14:52:45 EDT