Important Note
This server is no longer maintained and updated. We are planning an entire relaunch of the service with considerably more features until the end of 2008. Please be sure to check our Services page at http://www.came.sbg.ac.at for further details and continuous updates.
Description
QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins). QSCOP endows classic SCOP Families with quantified structural information which classic SCOP does not provide. Moreover, QSCOP is concurrent with PDB (the Protein Data Base), containing all protein structures currently available. Although BLAST is a sequence comparison tool, any strong or weak hit found in QSCOP retrieves the complete set of structural homologues classified in QSCOP. The structural diversity and redundancy of the proteins retrieved may be controlled by the user.
Usage
Insert your protein sequence in FASTA format in the text field on the left side, and select the classification layer from the drop down menu to reduce redundancy. The Domain layer results are equal to non-filtered lists whereas the selection of the Distant layer results in hit lists with the lowest redundancy.
The given standard BLAST parameters are explained on the BLAST webpage, except the Iterations drop down box, which allows the selection of the PSI-BLAST iterations (1 is equivalent to a standard BLAST run).
On the result list you can superimpose and display two structures by marking the accordant check boxes (currently unavailable).
