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The DomainFinder User's Manual comes with the DomainFinder code. It is also available on-line and for downloading in PostScript format.

DomainFinder is based on new theoretical methods which permit the identification of dynamical domains from a single conformation with almost negligible computational effort. This is due to a simplified normal mode calculation technique, which is described in detail in

K. Hinsen
Analysis of domain motions by approximate normal mode calculations
Proteins 33(3), 417-429 (1998)

The other theoretical methods developed for DomainFinder, as well as some example applications, are covered in

K. Hinsen, A. Thomas, M.J. Field
Analysis of domain motions in large proteins
Proteins 34(3), 369-382 (1999)