QSCOP-BLAST--fast retrieval of quantified structural information for protein sequences of unknown structure.
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/
Suhrer
Stefan J
SJ
Center of Applied Molecular Engineering, Department of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria.
Gruber
Markus
M
Sippl
Manfred J
MJ
D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D020407:Internet; D008956:Models, Chemical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020027:Pyrococcus furiosus / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D020124:Thermotoga maritima / Q000378:metabolism
D011506:Proteins