I have a small scaffold and would like to find compounds that contain the same or similar shape. Is there a way to do this using Schrödinger software?

This should be possible using Phase Shape Screening. In the Options panel of the Shape Screening panel, set the "Similarity normalization" to "Query structure", and set the similarity threshold to a high value. Setting this to 0.9, for instance will, roughly speaking, identify screening structures that can overlap with 90% of the scaffold.

Keywords: Maestro

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