ASH (Alignment of Structural Homologs) is a structure alignment program that has been developed for PDBj.  Earlier versions of ASH were written by Hiroyuki Toh[1]. The core alignment algorithm based on the double dynamic programming algorithm of Orengo and Taylor[2] was then combined with a new scoring function based on NER (Number of Equivalent Residues) by Daron M. Standley[3,4]. This page serves as a central portal where both web services and source code can be accessed.

 

ASH Web services

 

The Toh Lab at Kyoto University provides tools for mapping functional information from alignments as well as the original versions of local and global ASH.

 

RASH Rapid ASH computes pair-wise alignments in under 1 second. RASH is generally sufficient if the structures are very similar.

 

GASH 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.

 

ASH Source Code

 

ASH 1.0 is freely available.  You must fill out a simple license agreement, then a link containing the source code will be sent to you by e-mail.

 

[1]       Toh, H. (1997) Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm. Comput Appl Biosci 13, 387-96.

[2]       Orengo, C.A. and Thornton, J.M. (2005) Protein families and their evolution-a structural perspective. Annu Rev Biochem 74, 867-900.

[3]       Standley, D.M., Toh, H. and Nakamura, H. (2004) Detecting local structural similarity in proteins by maximizing number of equivalent residues. Proteins 57, 381-91.

[4]       Standley, 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.