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Article ID: 180 - Last Modified: May 4, 2011

How can I easily dock a library of homologous molecules?

If you know how the compounds are meant to bind then Glide's core constraints provide a useful mechanism for restraining the common parts of the molecule, while exploring the new functional groups.

The core constraints are set up in the docking stage of a Glide calculation. You should restrict the docking to a reference position with an RMS between 0.6 and 1.0 Å (the exact value depends on the variability you expect or have observed: too low a value will result in Glide returning few if any poses, too large a value will essentially result in the filter doing nothing). You can easily specify the common scaffold to be used as a SMILES string, but be careful to only include the sections of the molecule that are genuinely common and ensure that you haven't accidentally included H-atoms that will be substituted later.

It may be advisable to generate some additional conformations of your input molecules prior to docking if Glide is struggling to match the core constraints.

Keywords: Glide, core constraints, library docking.

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