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Nucleic Acids Res. 2012 Jul;40(Web Server issue):W257-62. doi: 10.1093/nar/gks555. Epub 2012 Jun 12.

BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles.

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1
University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland. dgront@chem.uw.edu.pl

Abstract

The BioShell package has recently been extended with a web server for protein homology detection based on profile-to-profile alignment (known as 1D threading). Its aim is to assign structural templates to each domain of the query. The server uses sequence profiles that describe observed sequence variability and secondary structure profiles providing expected probability for a certain secondary structure type at a given position in a protein. Three independent predictors are used to increase the rate of successful predictions. Careful evaluation shows that there is nearly 80% chance that the query sequence belongs to the same SCOP family as the top scoring template. The Bioshell Threader server is freely available at: http://www.bioshell.pl/threader/.

PMID:
22693216
PMCID:
PMC3394251
DOI:
10.1093/nar/gks555
[Indexed for MEDLINE]
Free PMC Article
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