文献类型：期刊文献

中文题名：基于等值面的分子溶剂可及表面快速生成算法

英文题名：Fast Solvent-Accessible Surface Generation Algorithm Based on iso-Contouring

作者：龚家瑜[1];高大启[1];李洪林[1,2]

机构：[1]华东理工大学信息科学与工程学院,上海200237;[2]华东理工大学药学院,上海200237

年份：2013

卷号：39

期号：5

起止页码：610

中文期刊名：华东理工大学学报（自然科学版）

外文期刊名：Journal of East China University of Science and Technology

收录：CSTPCD;;Scopus;北大核心:【北大核心2011】；CSCD:【CSCD2013_2014】；

基金：国家"863"项目(2012AA020308)

语种：中文

中文关键词：分子溶剂可及表面;等值面;高斯滤波;移动立方体

外文关键词：molecular solvent-accessible surface; iso-contouring; Gaussian filter; marching cubes

摘要：分子表面的描述在蛋白-蛋白、蛋白-配体相互作用分析中起着关键的作用。为此,本研究设计了基于等值面原理的分子溶剂可及表面生成程序并进行了性能测试。该程序采用一维递归快速高斯滤波计算方法,在三维离散空间中快速构造等值面,利用等值面提取技术(Marching Cubes)获取以三角面片表示的分子溶剂可及表面,并使用中心差分法计算三角面片的法向量,从而获得更好的显示效果。实际测试结果表明,该算法计算速度较快,准确性良好,可为基于结构的靶标识别方法提供有效药物靶标的分子表面表征。目前该程序已经被整合入国产大型药物设计图形软件包D^3 Pharma中。
Description of molecular shape plays an important role in the analysis of protein-protein and protein-ligand interactions. By means of Go surface theory, this paper proposes a molecular solvent accessible surface generation program and makes the corresponding efficiency tests. The proposed method adopts a rapid one dimensional recursive Gaussian filter algorithm, in which the iso-surface is constructed in the discrete three dimensional spaces and the molecular solvent-accessible surface of triangle representations by using iso-surface extraction technique ＂Marching Cubes＂. Moreover, the central difference method is utilized to calculate the normal vector of triangles such that a better render effect is achieved. The experimental results show that the present method has faster speed and higher accuracy of computation, and can provide effective drug target surface representations for structure-based target identifications. Now, this proposed program has been integrated into the software package, D3 Pharma.