KNOTTIN: The knottin or inhibitor cystine knot scaffold in 2007

Gracy, Jérôme, Le Nguyen, Dung, Gelly, Jean Christophe, Kaas, Quentin, Heitz, Annie and Chiche, Laurent (2008) KNOTTIN: The knottin or inhibitor cystine knot scaffold in 2007. Nucleic Acids Research, 36 SUPPL. 1: D314-D319. doi:10.1093/nar/gkm939


Author Gracy, Jérôme
Le Nguyen, Dung
Gelly, Jean Christophe
Kaas, Quentin
Heitz, Annie
Chiche, Laurent
Title KNOTTIN: The knottin or inhibitor cystine knot scaffold in 2007
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 1362-4962
0305-1048
Publication date 2008-01-01
Year available 2008
Sub-type Article (original research)
DOI 10.1093/nar/gkm939
Open Access Status DOI
Volume 36
Issue SUPPL. 1
Start page D314
End page D319
Total pages 6
Place of publication Oxford
Publisher Oxford University Press
Language eng
Subject 060102 Bioinformatics
Abstract The KNOTTIN database provides standardized information on the small disulfide-rich proteins with a knotted topology called knottins or inhibitor cystine knots. Static pages present the essential historical or recent results about knottin discoveries, sequences, structures, syntheses, folding, functions, applications and bibliography. New tools, KNOTER3D and KNOTER1D, are provided to determine or predict if a user query (3D structure or sequence) is a knottin. These tools are now used to automate the database update. All knottin structures and sequences in the database are now standardized according to the knottin nomenclature based on loop lengths between knotted cysteines, and to the knottin numbering scheme. Therefore, the whole KNOTTIN database (sequences and structures) can now be searched using loop lengths, in addition to keyword and sequence (BLAST, HMMER) searches. Renumbered and structurally fitted knottin PDB files are available for download as well as renumbered sequences, sequence alignments and logos. The knottin numbering scheme is used for automatic drawing of standardized two-dimensional Colliers de Perles of any knottin structure or sequence in the database or provided by the user. The KNOTTIN database is available at http://knottin.cbs.cnrs.fr.
Keyword Biochemistry & Molecular Biology
Biochemistry & Molecular Biology
BIOCHEMISTRY & MOLECULAR BIOLOGY
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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