Nucleic Acids Research Advance Access originally published online on November 19, 2007
Nucleic Acids Research 2008 36(Database issue):D314-D319; doi:10.1093/nar/gkm939
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, Database issue D314-D319
© 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.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007
1Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale, 34090 Montpellier, 2INSERM, U554, Montpellier, 3CNRS, FRE3009; BIORAD; Complex system modelling and engineering for diagnostic, Montpelllier, 4CNRS, UPR 9080, Université Paris 7, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, France and 5Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
*To whom correspondence should be addressed. Tel: +(33) 4 67 41 77 03; Fax: +(33) 4 67 41 79 13; Email: laurent.chiche{at}cbs.cnrs.fr
Received September 14, 2007. Revised October 8, 2007. Accepted October 11, 2007.
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.