title: The KNOTTIN website and database: a new information system dedicated to the knottin scaffold.
abstract: The KNOTTIN website and database organize information about knottins or inhibitor cystine knots, small disulfide-rich proteins with a knotted topology. Thanks to their small size and high stability, knottins provide appealing scaffolds for protein engineering and drug design. Static pages present the main historical and recent results about knottin discoveries, sequences, structures, folding, functions, applications and bibliography. Database searches provide dynamically generated tabular reports or sequence alignments for knottin three-dimensional structures or sequences. BLAST/HMM searches are also available. A simple nomenclature, based on loop lengths between cysteines, is proposed and is complemented by a uniform numbering scheme. This standardization is applied to all knottin structures in the database, facilitating comparisons. Renumbered and structurally fitted knottin PDB files are available for download. The standardized numbering is used for automatic drawing of two-dimensional Colliers de Perles. The KNOTTIN website and database are available at http://knottin.cbs.cnrs.fr and http://knottin.com.
authors.affiliation: Centre de Biochimie Structurale, UMR 5048 CNRS INSERM Université Montpellier I, Faculté de Pharmacie, 15 avenue Charles Flahault, F-34093 Montpellier, France.
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Gelly
authors.forename: Jérôme
authors.initials: J
authors.lastname: Gracy
authors.forename: Quentin
authors.initials: Q
authors.lastname: Kaas
authors.forename: Dung
authors.initials: D
authors.lastname: Le-Nguyen
authors.forename: Annie
authors.initials: A
authors.lastname: Heitz
authors.forename: Laurent
authors.initials: L
authors.lastname: Chiche
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D003553:Cystine / Q000737:chemistry*; D030562:Databases, Protein; D004220:Disulfides / Q000737:chemistry*; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship; D009626:Terminology as Topic
chemical_list: D004220:Disulfides; D011506:Proteins; D003553:Cystine