Is there anyway to find good-docking compounds that are dissimilar to my known actives?

One option is to use similarity scoring within Glide itself (the Similarity tab of the Ligand Docking panel). With this feature, you can penalize the GlideScore of docked ligands that are similar (or dissimilar) to a supplied set of known actives.

You could also use Canvas to find ligands that are dissimilar to the active set, either from the input ligands before docking, or from the docked ligands. To do this, you can use the utilities

$SCHRODINGER/utilities/canvasFPGen
$SCHRODINGER/utilities/canvasDBCS

The first program generates fingerprints for compounds. You can do this for the active set, and for the docked ligands or the input ligands. The second program selects a subset of dissimilar compounds from a database. If you use the '-ifp' option to specify the docking input or results fingerprints, and the '-ifp2' option to specify the active set fingerprints, the program generates a diverse set of compounds that avoids the chemical space of the active set.

Keywords: dissimilarity analysis, similarity scoring, canvas, dissimilar ligands, Glide

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