Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
复制标题
DOI：
10.1110/ps.0368703
复制
发表时间：
2003-08-01
期刊：
影响因子：
8
通讯作者：
Nakamura, H
中科院分区：
文献类型：
--
作者：
Kinoshita, K;Nakamura, H
在后基因组测序时代，基于蛋白质三维结构的生物化学功能鉴定是一个迫切的需求。我们发展了一种新的方法来识别和预测蛋白质的生化功能，利用分子表面的几何形状和表面上的静电势的相似性信息。我们的预测系统包括一个相似性搜索方法的基础上的团搜索算法和分子表面数据库EF-网站（静电表面的功能网站在蛋白质）。使用该系统，在几种具有不同折叠的单抗结合蛋白中检测到类似于磷酸烯醇丙酮酸羧基激酶的功能位点。我们还将我们的方法应用于来自詹氏甲烷球菌的假设蛋白质MJ 0226，并从与具有不同折叠的其他蛋白质的相似性检测了monlastide结合位点。
The identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database eF-site (electrostatic surface of functional-site in proteins). Using this system, functional sites similar to those of phosphoenoylpyruvate carboxy kinase were detected in several mononucleotide-binding proteins, which have different folds. We also applied our method to a hypothetical protein, MJ0226 from Methanococcus jannaschii, and detected the mononucleotide binding site from the similarity to other proteins having different folds.