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Pose Entropy

Schrödinger extension for KNIME Workbench version 20.3.139.202008121324 by Schrödinger

Computes a modified docking score based on the number of poses within each energy well. Input poses should come from Glide, saving 100 poses per ligand. The criteria for duplicate pose elimination should be reduced to zero (in the Clustering section under Advanced options in the Output tab of the Glide Docking panel) in order to ensure a full sampling of each energy well.

Platform Limitations: Linux only

Backend implementation

pose_entropy.py
The script pose_entropy.py is used to implement this node.

Options

Column containing structure
Select column in the data input table containing the structures
Distance cutoff
Sets distance at which clustering operation will end.
Energy property
Determines which Glide energy property forms the basis for the entropy calculation. This must be one of the following: emodel (default), cvdw, gscore (GlideScore), dockingscore (Docking Score)
Use energies
Use the energies to determine the probability of occurrence for a given pose in a cluster. Note that Ruvinsky does not do this in his original work.
Output the top scoring pose for each ligand
Output the top scoring pose for each cluster of poses for each ligand instead of only the overall top scoring pose for each ligand

Input Ports

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Input data table containing molecules in Maestro format

Output Ports

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Molecules in Maestro format

Views

Log output of pose_entropy.py
Log output of pose_entropy.py
Std out/err of pose_entropy.py
Std out/err of pose_entropy.py

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

KNIME 4.2
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Developers

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