Lai Yan-Long, Yen Shih-Chung, Yu Sung-Huan, Hwang Jenn-Kang
Institute of Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W420-4. doi: 10.1093/nar/gkm304. Epub 2007 May 25.
Knotted proteins are more commonly observed in recent years due to the enormously growing number of structures in the Protein Data Bank (PDB). Studies show that the knot regions contribute to both ligand binding and enzyme activity in proteins such as the chromophore-binding domain of phytochrome, ketol-acid reductoisomerase or SpoU methyltransferase. However, there are still many misidentified knots published in the literature due to the absence of a convenient web tool available to the general biologists. Here, we present the first web server to detect the knots in proteins as well as provide information on knotted proteins in PDB-the protein KNOT (pKNOT) web server. In pKNOT, users can either input PDB ID or upload protein coordinates in the PDB format. The pKNOT web server will detect the knots in the protein using the Taylor's smoothing algorithm. All the detected knots can be visually inspected using a Java-based 3D graphics viewer. We believe that the pKNOT web server will be useful to both biologists in general and structural biologists in particular.
近年来，由于蛋白质数据库（PDB）中结构数量的急剧增加，打结蛋白质越来越常见。研究表明，结区域对蛋白质中的配体结合和酶活性都有贡献，例如植物色素的发色团结合结构域、酮醇酸还原异构酶或SpoU甲基转移酶。然而，由于缺乏方便普通生物学家使用的网络工具，文献中仍有许多错误识别的结。在这里，我们展示了第一个用于检测蛋白质中的结以及提供PDB中打结蛋白质信息的网络服务器——蛋白质KNOT（pKNOT）网络服务器。在pKNOT中，用户可以输入PDB ID或上传PDB格式的蛋白质坐标。pKNOT网络服务器将使用泰勒平滑算法检测蛋白质中的结。所有检测到的结都可以使用基于Java的3D图形查看器进行可视化检查。我们相信，pKNOT网络服务器对普通生物学家尤其是结构生物学家都将是有用的。
