Alignment of
Structural Homologs

is a structure alignment program that has been developed for PDBj.
Earlier versions of ASH were written by Hiroyuki Toh1.
The core alignment algorithm based on the double dynamic programming algorithm of Orengo and Taylor2 was then combined with a new scoring function based on NER (Number of Equivalent Residues) by Daron M. Standley3,4.

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Rapid ASH computes pair-wise alignments in under one second. RASH is generally sufficient if the structures are very similar.


Genetic-algorithm ASH generates very accurate alignments in about twice the time as RASH. GASH is the best choice if the structures are only partially similar or if multiple solutions are required.


DASH is a database built from ASH structural alignments of all known structurally homologous protein domains and chains in the PDB.

1Toh, H. (1997) Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm. Comput Appl Biosci 13, 387-96. 2Orengo,C.A. and Thornton, J.M. (2005) Protein families and their evolution-a structural perspective. Annu Rev Biochem 74, 867-900. 3Standley,D.M., Toh, H. and Nakamura, H. (2004) Detecting local structural similarity in proteins by maximizing number of equivalent residues. Proteins 57, 381-91. 4Standley,D.M., Toh, H. and Nakamura, H. (2005) GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures.BMC Bioinformatics 6, 221.