Classification of ligand molecules in PDB with graph match-based structural superposition.
Classification of ligand molecules in PDB with graph match-based structural superposition.
复制标题
使用基于图匹配的结构叠加对 PDB 中的配体分子进行分类。
DOI：
10.1007/s10969-016-9209-x
复制
发表时间：
2016
期刊：
影响因子：
--
通讯作者：
T.
中科院分区：
文献类型：
--
作者：
Shionyu-Mitsuyama;C.;Hijikata;A.;Tsuji;T. & Shirai;T.
通过添加结构叠加过程来验证原子-原子匹配，对小分子快速启发式图匹配算法 COMPLIG 进行了改进。采用改进的方法对蛋白质数据库（PDB）中的小分子配体进行三维结构分类，将PDB中的16,660种配体分为7561个簇。相比之下，通过先前方法（无结构叠加）进行的分类从同一配体组生成了 3371 个簇。当前分类系统的特征是单簇数量增加，簇中仅包含一个配体分子。对当前分类系统中而非前一分类系统中的单例的检查表明，分离的主要因素是手性、循环构象、子结构分离和键长的差异。当前和以前的分类系统之间的比较表明，由于原子-原子匹配的严格性，基于叠加的分类在功能相关配体的聚类方面是有效的，例如针对特定生物过程的药物。
The fast heuristic graph match algorithm for small molecules, COMPLIG, was improved by adding a structural superposition process to verify the atom–atom matching. The modified method was used to classify the small molecule ligands in the Protein Data Bank (PDB) by their three-dimensional structures, and 16,660 types of ligands in the PDB were classified into 7561 clusters. In contrast, a classification by a previous method (without structure superposition) generated 3371 clusters from the same ligand set. The characteristic feature in the current classification system is the increased number of singleton clusters, which contained only one ligand molecule in a cluster. Inspections of the singletons in the current classification system but not in the previous one implied that the major factors for the isolation were differences in chirality, cyclic conformations, separation of substructures, and bond length. Comparisons between current and previous classification systems revealed that the superposition-based classification was effective in clustering functionally related ligands, such as drugs targeted to specific biological processes, owing to the strictness of the atom–atom matching.