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International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 25.1, p. 692
Section 25.1.8.5. NACCESS
a
Biomolecular Crystallography Laboratory, CABM & Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA, and Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Yue-Yang Road, Shanghai 200 031, People's Republic of China, and bBiomolecular Crystallography Laboratory, CABM & Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA |
NACCESS
is a stand-alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessibility for both proteins and nucleic acids. The program uses the Lee & Richards (1971)![[link]](/graphics/greenarr.gif)
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 Å) 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. The output from the program can also be read in by HBPLUS (Section 25.1.8.2) and LIGPLOT (Section 25.1.9.2).
Location: http://wolf.bms.umist.ac.uk/naccess/ . Operating systems: UNIX, SGI, Sun, HP, DEC and LINUX. Type: source code. Language: Fortran77. Distribution: free academic.
References
Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379–400.Google Scholar
