schrondinger蛋白 小分子构象聚类

首先把蛋白构象导入到project table中

然后在conformers中计算RMSD matrix。 可以整个蛋白也可以指定氨基酸计算RMSD matrix

计算完rmsd matrix ，就可以执行 calculate clustering。然后在results中获得聚类的分析，比如聚类树，聚类热图，聚类个数的kelly分析。在apply中提取每一类的代表构象

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统计每一类中的成员个数，

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计算RMSD耗时特别长，随着蛋白构象数目的增加，时间呈现指数增加。

RMSD计算完后会产生相应的csv文件，该csv文件记录了相应的RMSD数据，可以直接载入。

如图

从而可以直接聚类。

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What is the Kelley criterion in Canvas Hierarchical Clustering?

The Kelley index is a criterion to select an optimal number of  clusters. The Kelley measure balances the normalized "spread" of the clusters at a particular level with the number of clusters at that level.

The clustering level with the lowest penalty represents a state where the clusters are as highly populated as possible, while simultaneously maintaining the smallest spread. The smaller the spread of the clusters, the more similar are the conformations of its members; the greater the population of a cluster, the smaller is the chance of excluding a member of similar conformation.