A program to search for 3D fragments similar to (fragments of) a query structure.
This will convert 3D file(s) (PDB format) into a 1D encoding of a 27 state structural alphabet (HMM learnt). This HMM-SA sequence will then be used to search for similarities, using standard alignment techniques such as Smith & Waterman algorithm or suffix trees.
More information on HMM structural alphabets here
Some graphical visualization of HMM encoding here
Note: since the encoding of conformations uses HMM, protein having several fragments cannot be treated as a whole. Instead, several independent searches (one per fragment) will be performed.
Additional help about this service
Last bank update: June 2006