A method for fast approximate searching of polypeptide structures in the PDB

Abstract

The main contribution of this paper is a novel approach for fast searching in huge structural databases like the PDB. The data structure is based on an adaption of the generalized suffix tree and relies on an translationand rotation-invariant representation of the protein backbone. The method was evaluated by applying structural queries to the PDB and comparing the results to the established tool SPASM. Our experiments show that the new method reduces the query time by orders of magnitude while producing comparable results.