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

ASH Web services

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

RASH Rapid ASH computespair-wise alignments in under 1 second. RASH is generally sufficient if thestructures are very similar.

GASH Genetic-algorithm ASHgenerates very accurate alignments in about twice the time as RASH. GASH is thebest choice if the structures are only partially similar or if multiplesolutions are required.

ASH Source Code

ASH 1.2 (fixed some long-standing bugs present in ver 1.0) is freelyavailable. You must fill out asimple license agreement, then a link containing the source code will be sentto you by e-mail.

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

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

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

[4] Standley,D.M., Toh, H. and Nakamura, H. (2005) GASH: an improved algorithm formaximizing the number of equivalent residues between two protein structures.BMC Bioinformatics 6, 221.