Gelly Jean-Christophe, Gracy Jérôme, Kaas Quentin, Le-Nguyen Dung, Heitz Annie, Chiche Laurent
Centre de Biochimie Structurale, UMR 5048 CNRS INSERM Université Montpellier I, Faculté de Pharmacie, 15 avenue Charles Flahault, F-34093 Montpellier, France.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D156-9. doi: 10.1093/nar/gkh015.
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.
KNOTTIN网站和数据库整理了有关结蛋白或抑制剂胱氨酸结的信息,结蛋白是一类富含二硫键的小型蛋白质,具有打结的拓扑结构。由于其体积小且稳定性高,结蛋白为蛋白质工程和药物设计提供了有吸引力的支架。静态页面展示了有关结蛋白发现、序列、结构、折叠、功能、应用及参考文献的主要历史和最新成果。数据库搜索可为结蛋白的三维结构或序列提供动态生成的表格报告或序列比对。也可进行BLAST/HMM搜索。我们提出了一种基于半胱氨酸之间环长度的简单命名法,并辅以统一的编号方案。这种标准化应用于数据库中的所有结蛋白结构,便于进行比较。重新编号并进行结构拟合的结蛋白PDB文件可供下载。标准化编号用于自动绘制二维珍珠项链图。KNOTTIN网站和数据库可通过http://knottin.cbs.cnrs.fr和http://knottin.com访问。