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Naccess


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Naccess calculates the atomic accessible area when a probe is rolled around the Van der Waal's surface of a macromolecule. Such 3-dimensional co-ordinate sets (PDB files) are available from RCSB. The program uses the Lee & Richards method, whereby a probe of given radius is rolled around the surface of the molecule, and the path traced out by its centre is the accessible surface. Typically, the probe has the same radius as water (1.4 Angstroms) and hence the surface described is often referred to as the solvent accessible surface. The calculation makes successive thin slices through the 3D molecular volume to calculate the accessible surface of individual atoms, and hence is an approximation - thinner slices improves the accuracy.

http://www.bioinf.manchester.ac.uk/naccess/



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