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Does Schrödinger software include scaffold clustering?

There is not currently such a feature. However, Canvas, the cheminformatics platform, has some similarly useful tools.

First, try CanvasMCS, the maximum common substructure facility. You can specify a minimum and maximum number of structures that must match in order to find common scaffolds in a dataset. Use the checkbox "Enforce minimum size" to avoid generating small substructures.

For up to a few thousand structures, you can also try Hierarchical Clustering. After the initial clustering step, select clusters at the Kelley level. Every cluster may not share a common scaffold, but this method does a very good job of separating compounds into different chemical classes.

For larger numbers of compounds, there is Leader-Follower clustering. Experiment with the size of the cluster radius to get clusters that are sufficiently homogeneous without a large population of singletons. There is also K-Means clustering. You can specify the number of clusters in advance.

Finally, the R-Group Analysis tool can also be useful. This tool is included in both Maestro (Tools menu) and Canvas (Scripts menu).

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