GANGSTA+ is a combinatorial algorithm for non-sequential structural alignment of proteins and similarity search in databases developed by A. Guerler et al. incorporating findings of B. Kolbeck and P. May.

We provide a database of protein structures that are sequentially or non-sequentially similar generated by evaluating all-versus-all structure alignments of a representative set of protein structures. Since GANGSTA+ ignores the polypeptide chain connectivity of SSEs (secondary structure elements), it is able to detect structural similarities between two proteins, although their sequences might be reshuffled during evolution. We applied GANGSTA+ in an all-against-all comparison on the ASTRAL40 database (SCOP version 1.75), which consists about 10.000 protein domains yielding about 50 million possible protein structure alignments. Here, we provide the resulting protein structure alignments as a public web-based database, named GDB (GANGSTA+ Database). The GDB allows a comprehensive analysis of protein structure families according to the SCOP classification scheme. Additionally users are enabled to upload their own protein structures for pair-wise protein structure comparison or alignment against all protein structures of the ASTRAL40 database (SCOP version 1.75).

Tracking of Submitted Queries (updated: 2009-06-12)

Recent Updates and Changes

• 2009-10-02 : Default configuration of web service changed. Assignment of secondary structure elements in same sequential order only.
• 2009-10-02 : Inclusion of the SSE assignment heuristic described by Zhang and Skolnick.
• 2009-10-01 : Inclusion of the Kabsch implementation of Bosco.
• 2009-03-24 : Default configuration of web service changed. Accepted RMSD cut off increased.