Clustering of docked poses

Hi there,
I am dealing with a large set of poses (>10000) made in MAESTRO Schrödinger. Poses are coming from different types of structures which are different than the native ligand that was found in the protein. I would like to perform different types of clustering to find best ones, yet I don’t know how to do it. I already did Interaction fingerprint clustering, but I would like to do the RMSD as well. Is there a workflow which calculates it and like workflow in general that can be used for this purpose?

Hi @nejraG ,
I am not an expert in this field, but I came across a similar workflow on the KNIME HUB
Cocrystallized Ligand Redocking – KNIME Community Hub by @Schroedinger which might help you?

You could also have a look at some of the other workflows by @Schroedinger in this space.

Let us know if it worked for you.


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Just a quick note to say that there are various ways to cluster poses.
You mentioned you already clustered according to interaction fingerprints you can also use the Cluster Ligands panel in Maestro which can also be added to a Knime workflow as needed. You can also cluster according to similar scaffold for which we have a command line script that can be added to a Knime workflow through the use of the Chemistry External Tool node.
If you can contact us directly by emailing, we would be happy to help you with this further anytime.
Many thanks,

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