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Strain Rescore

Schrödinger extension for KNIME Workbench version 20.3.139.202008121324 by Schrödinger

Calculates penalties for eccentric pose geometries. For each ligand pose in the input, a tightly constrained minimization and an unconstrained minimization is performed with MacroModel. The energy difference is used to determine the Glide gscore penalty.

The output will contain the original properties plus:
    1) the potential energy of constrained geometry, calculated without
    constraints.
    2) the potential energy of fully minimized geometry, starting from
    the constrained optimization's coordinates.
    3) the difference between these two potentials;  the ligand strain
    4) the modified Glide docking score (strain_glide_gscore)

Platform Limitations: The maximum number of subjobs that can be run on Windows is 1. This should be modified in the 'Job Control tab', by selecting the "Number of subjobs" checkbox and editing the value to '1'.

Backend implementation

$SCHRODINGER/run strain_rescore.py
The script strain_rescore.py is used to implement this node.

Options

Column containing input
Select the column containing Pose Viewer input
Energy Offset
Ignored strain energy threshold. Default is 4.00 kcal/mol
Scale factor
Penalty scale factor. Default is 0.25
Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: StrainRescore
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option without a value, specify the option_name and the value as _off_ through the flow variable.

To remove an existing option with a value, specify the option_name and the value as _rm_ through the flow variable.

Input Ports

Icon
Pose viewer in Maestro format

Output Ports

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Molecules with added properties in Maestro format

Views

Log output of Strain Rescore
Log output of Strain Rescore

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

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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