Search for 3D fragments similar to (fragments of) a protein query structure.
Highlights:
It can be used to mine for protein structures and extract structural similarities.
It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of 3D protein conformations into a 1D representation using a limited number of prototype conformations.
SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem.
