eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
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DOI：
10.1093/nar/gkm351
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发表时间：
2007-07-01
影响因子：
14.9
通讯作者：
Nakamura, Haruki
中科院分区：
文献类型：
--
作者：
Kinoshita, Kengo;Murakami, Yoichi;Nakamura, Haruki
我们开发了一种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配体结合位点的方法。根据分子表面的形状和它们的静电势来测量相似性。一个新的Web服务器，eF-seek，提供了一个接口，我们的搜索方法。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一个虚拟的复杂结构，与PDB格式文件中的推定配体作为输出。此外，显示预测的交互界面，以便于在我们自己的applet查看器上用网络浏览器（URL：http：//eF-site.hgc.jp/eF-seek）检查虚拟复杂结构。
We have developed a method to predict ligandbinding 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).