基于结构比对蛋白结合位点预测方法①.PDFVIP

2015 年 第 24 卷 第 10 期 计 算 机 系 统 应 用 基于结构比对的蛋白结合位点预测方法① 刘广钟, 朱佳莉 (上海海事大学 信息工程学院, 上海 201306) 摘 要: 蛋白质通过结合位点与其他分子产生相互作用, 所以对蛋白结合位点的预测具有重要的意义. 现有许多 不同的预测方法, 但是这些方法存在命中率低或计算量大的问题, 本文引入了一种基于结构比对的蛋白质位点 预测方法, 同时在结构比对过程中引入同源索引, 找出相应的同源模版, 并与之进行结构比对, 然后将结构相似 的模版中的配体映射到目标蛋白质中, 采用聚类方法对位点进行分析. 结果表明, 与其他预测方法相比, 本文的 方法降低了计算量, 并提高了预测精度. 关键词: 结合位点; 同源索引; 结构比对; 聚类 Binding Sites Prediction Method Based on Structural Alignment LIU Guang-Zhong, ZHU Jia-Li (Shanghai Martime University, Information Engineering College, Shanghai 201306, China) Abstract: Proteins interact with other molecules through binding sites, so it is significant to identify protein binding sites. Although there are different computational methods for the identification of binding sites, the existing prediction methods have problems of low hit rate or large computation. In this paper, a binding sites prediction method based on structural alignment is introduced. In the process of structural alignment, homologous index is applied to screening out homologous templates, with which query chains are aligned, and then the ligands in similar structure templates are mapped onto the query chains. Clustering method is used for analysis of sites. The result indicates that reduced computation and improved prediction accuracy, compared with other prediction methods, can be obtained through our method. Key words: binding sites; homologous index; structural alignment; clustering [2] 蛋白质是生命物质的基础, 是构成生命体的基本 的凹槽, 把最大凹槽处的残基作为蛋白质的结合位点 . 成分. 蛋白质也是生命功能活动的执行者, 主要通过 POCKET[3] 、LIGSITE[4] 、PASS[5] 、SURFNET[6] 、CAST[7