SA-Search v1.0

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

Query:

Against:
PDBid
PDBid
PDB File
PDB File
Information about the lists
PDB:

Search parameters:
Search method:
Minimal Match Length:
RMSd max :
Maximal number of matches :
Minimal Score (0. - 1.):
search using amino acid sequence (instead of HMM encoding sequence)
Return :

send result by email (optional)
Email address: