Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan, Republic of China.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W228-31. doi: 10.1093/nar/gks592. Epub 2012 Jun 12.
Knotted proteins have recently received lots of attention due to their interesting topological novelty as well as its puzzling folding mechanisms. We previously published a pKNOT server, which provides a structural database of knotted proteins, analysis tools for detecting and analyzing knotted regions from structures as well as a Java-based 3D graphics viewer for visualizing knotted structures. However, there lacks a convenient platform performing similar tasks directly from 'protein sequences'. In the current version of the web server, referred to as pKNOT v.2, we implement a homology modeling tool such that the server can now accept protein sequences in addition to 3D structures or Protein Data Bank (PDB) IDs and return knot analysis. In addition, we have updated the database of knotted proteins from the current PDB with a combination of automatic and manual procedure. We believe that the updated pKNOT server with its extended functionalities will provide better service to biologists interested in the research of knotted proteins. The pKNOT v.2 is available from http://pknot.life.nctu.edu.tw/.
由于其有趣的拓扑新颖性及其令人费解的折叠机制，纽结蛋白最近受到了广泛关注。我们之前发布了一个 pKNOT 服务器，它提供了一个纽结蛋白的结构数据库，用于从结构中检测和分析纽结区域的分析工具，以及一个基于 Java 的 3D 图形查看器，用于可视化纽结结构。然而，缺乏一个方便的平台，可以直接从“蛋白质序列”执行类似的任务。在当前版本的网络服务器中，称为 pKNOT v.2，我们实现了同源建模工具，使得服务器现在除了 3D 结构或蛋白质数据库 (PDB) ID 之外，还可以接受蛋白质序列，并返回结分析。此外，我们还使用自动和手动程序的组合更新了当前 PDB 中的纽结蛋白数据库。我们相信，具有扩展功能的更新的 pKNOT 服务器将为对纽结蛋白研究感兴趣的生物学家提供更好的服务。pKNOT v.2 可从 http://pknot.life.nctu.edu.tw/ 获取。
