Knowledge Base

Article ID: 210 - Last Modified:

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).

Back to Search Results

Was this information helpful?

What can we do to improve this information?


To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles