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Nucleic Acids Research Advance Access published online on May 3, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm264
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

QSCOP-BLAST—fast retrieval of quantified structural information for protein sequences of unknown structure

Stefan J. Suhrer, Markus Gruber and Manfred J. Sippl*

Center of Applied Molecular Engineering, Department of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria

*To whom correspondence should be addressed. Tel: 0043-662-8044-5796; Fax: 0043-662-8044-176; Email: sippl{at}came.sbg.ac.at

Received January 31, 2007. Revised March 30, 2007. Accepted April 8, 2007.

QSCOP is a quantitative structural classification of proteins which distinguishes itself from other classifications by two essential properties: (i) QSCOP is concurrent with the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank and (ii) QSCOP covers the widely used SCOP classification with layers of quantitative structural information. The QSCOP-BLAST web server presented here combines the BLAST sequence search engine with QSCOP to retrieve, for a given query sequence, all structural information currently available. The resulting search engine is reliable in terms of the quality of results obtained, and it is efficient in that results are displayed instantaneously. The hierarchical organization of QSCOP is used to control the redundancy and diversity of the retrieved hits with the benefit that the often cumbersome and difficult interpretation of search results is an intuitive and straightforward exercise. We demonstrate the use of QSCOP-BLAST by example. The server is accessible at http://qscop-blast.services.came.sbg.ac.at/


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