Clark D E, Willett P, Kenny P W
Department of Information Studies, University of Sheffield, UK.
J Mol Graph. 1992 Dec;10(4):194-204. doi: 10.1016/0263-7855(92)80068-o.
This paper discusses the use of bounded distance matrices for the representation of conformationally flexible three-dimensional (3D) molecules. It is shown that pharmacophoric pattern searches of databases of flexible 3D molecules represented in this way can be carried out using screen and geometric searching algorithms that are analogous to those used for searching databases of rigid 3D structures. Molecules matching a query pattern after the geometric search must then undergo a final conformational search to determine whether they can, in fact, adopt a conformation that matches the query. An analysis of this three-stage searching procedure shows that searching databases of flexible 3D molecules is extremely demanding of computational resources.
本文讨论了使用有界距离矩阵来表示构象灵活的三维（3D）分子。结果表明，对于以这种方式表示的灵活3D分子数据库进行药效团模式搜索时，可以使用类似于用于搜索刚性3D结构数据库的筛选和几何搜索算法来进行。在几何搜索后匹配查询模式的分子必须随后进行最终的构象搜索，以确定它们实际上是否能够采用与查询匹配的构象。对这个三阶段搜索过程的分析表明，搜索灵活3D分子数据库对计算资源的要求极高。
