Kinoshita Kengo, Murakami Yoichi, Nakamura Haruki
Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W398-402. doi: 10.1093/nar/gkm351. Epub 2007 Jun 12.
We have developed a method to predict ligand-binding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek).
我们开发了一种方法，通过在蛋白质数据库（PDB）中搜索相似的结合位点，来预测新蛋白质结构中的配体结合位点。根据分子表面的形状及其静电势来衡量相似性。一个新的网络服务器eF-seek提供了我们搜索方法的接口。它只需要一个PDB格式的坐标文件，并生成一个预测结果作为虚拟复合物结构，以PDB格式文件中的假定配体作为输出。此外，还会显示预测的相互作用界面，以便通过网络浏览器在我们自己的小程序查看器上检查虚拟复合物结构（网址：http://eF-site.hgc.jp/eF-seek）。
