A database search method should provide users to examine the statistical significance of an alignment to obtain an indication of the reliability of the prediction. Our 3D-BLAST is able to keep the advantages of BLAST tool and to provide E-value to users for fast structural database scanning. It searches for the longest common substructures, called SAHSPs (structural alphabet high-scoring segment pairs), existing between the query structure and every structure in the structural database. The SAHSP is similar to the high-scoring segment pair (HSP) in BLAST. 3D-BLAST is able to find all the protein structures of a database that share common substructures with a query structure.