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

Pose viewer in Maestro format

Output Ports

Molecules with added properties in Maestro format

Views

Log output of Strain Rescore

Log output of Strain Rescore

Best Friends (Incoming)

• Molecule Reader (to MAE) (50 %) 
• Glide Ligand Docking (17 %) Deprecated
• Pose Filter (17 %) 
• Split by Structure (17 %) 

Best Friends (Outgoing)

• Glide Grid Generation (33 %) 
• Molecule Writer (from MAE) (33 %) 
• Pose Filter (33 %) 

Workflows

• Parameter flow variables 1-2 (KNIME Hub) 
• Parameter flow variables 1-2 (KNIME Hub) 
• Parameter flow variables 1-2 (Schrödinger) 

Installation

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

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Developers

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