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I have a file of structures, and I would like to generate a subset of structures. What methods are available to me?

You can create a subset by filtering on one or more properties, using LigFilter. This tool is available in Maestro under Tools → Ligand Filtering, and from the command line as ligfilter.

You can generate a subset of structures by importing the file into Maestro, selecting entries in the Project Table and exporting the selected entries. Maestro supports random subsets as well as selection by property.

You can run a library optimization in Canvas (Applications → Hole Filling/Library Optimization), which selects a subset of compounds from a pool by minimizing their similarity, and optionally optimizing the ranges of specified properties. This tool can also be used to fill holes in an existing library of compounds.

You can generate a diverse subset based on fingerprints or properties, using the Diversity-Based Compound Selection application in Canvas.

Canvas can also perform clustering, and a representative structure from each cluster can be retrieved.

If you want to create a subset of structures in a Maestro or SD file from the command line by selection of structures according to their order in the file, you can use the utilities maesubset and sdsubset.

Related Articles:

#85: How do I cluster my ligand-like compounds, and choose a representative sample of each cluster?

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