BLAST search in Protein Data Bank

A common problem is to find solved structures that a similar to a sequence under study. Structures of homologous proteins can be used for approximate analysis of the structural features of the target protein, or as a starting point for modeling the structure of the unknown protein.

Data access component of Sirius allows for BLAST searches in the database of Protein Data Bank. The query is chosen from the display or sequence viewer. Alternatively, a local sequence file can be used. If it contains multiple sequences, the first one will be used as the query. At this time, PDB BLAST interface supports only protein searches (no DNA).

The search normally takes under one minute, but the exact time depends on the size of the sequence and parameters, such as cutoff value. Once the search is completed, the list of hits is displayed. The view shows PDB id, chains in the structure that are close matches, as well as E-value for each hit. Each structure can be loaded into Sirius, and the corresponding BLAST alignment can be viewed to assess the quality of the hit in addition to the E-value. Finally, the raw BLAST output file may be saved locally.