DASH stores ASH alignments of all known structurally homologous protein domains in a relational database. Every month the latest PDB entries are processed. The processing involves (a) clustering the entire PDB by sequence using cd-hit at 90% sequence identity; (b) decomposing the sequence representatives into domains using Protein Domain Parser (Alexandrov N, Shindyalov I. Bioinformatics 2003); (c) aligning all domains against all domains using RASH (Standley, D. M., Toh, H. & Nakamura, H. BMC Bioinformatics 2007) for those domain pairs that have not been previously processed; (d) storing the significant matches in DASH.
pdp domains stored in DASH
domain-domain alignments in DASH
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