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See Roach, et al., 2005 Proteins: Structure, Function, and Bioinformatics, 60:66-81 for one solution to this problem. I feel that this particular approach is stellar. Check Fig. 10 for an example of all-by-all superposition of 2400 snapshots from an MD trajectory, Fig. 9 for an example of the breadth of fidelity in comparing non-homologous structures, superfamilies, families, and different conformations of the same protein, and Fig. 7 for the identification of internal symmetry.
The software is not exactly user refractory, but is not available in a totally user-friendly environment, and Roach has left. The code is available, together with makefiles, minimal examples, and readme files.
**********UNCrystallographers NOTE new website url****************** [EMAIL PROTECTED] http://xtal.med.unc.edu/CARTER/Welcome.html Department of Biochemistry and Biophysics CB 7260 UNC Chapel Hill, Chapel Hill, NC 27599-7260 Tel: 919 966-3263 FAX 919 966-2852
