Prime MM-GBSA

The Prime MM-GBSA approach is used to predict the free energy of binding for a receptor and a set of ligands.

Backend implementation

Options

Column containing input structures

Select column in the data input table containing the structures

Output Column Structure

Choose the output column structure

Input plus Output - Input columns are included in the output
Output replaces Input - The column with output structures will replace the input column selected. Other input columns will be included in the output
Output only - Only Output structures

If any input column name is same as the output, then the input column name is suffixed with "_input"

Output type Select the output type

Output column name A custom output column name can be given by checking the checkbox ON and specifying the new column name

Extract properties Extract and add the additional properties generated by this node in the output as separate columns

Primary - Primary or most useful properties
All - All properties
None - No properties are extracted

Calculate ligand strain energies

Calculate ligand strain energies. Calculations are done on the free ligand and on the ligand in the geometry it adopts in the complex, both with implicit solvent. The strain energy is the difference between the two energies.

Use ligand input partial charges

If the ligand structure source has partial charges for the ligands, use these partial charges instead of those generated by the force field.

Size of flexible region in A

Select a range relative to the first input ligand for which protein atoms are allowed to move. The atoms in all residues within the specified distance of the first ligand processed are included in the flexible region.

Specify a receptor region using ASL

Designate a region of the receptor as flexible using an asl expression. (-receptor_region in prime_mmgbsa)

Select a sampling method

Choose a sampling method for the flexible protein residues. The default is to minimize them. You can instead choose to minimize just the side chains, to allow them to move in response to the ligand; or to minimize just the polar hydrogens, to optimize them for hydrogen bonding.

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: MMGBSA
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 from command line, just specify the option_name and the value as _off_ through the flow variable.

Views

Log output of MM-GBSA

Log output of MM-GBSA

Workflows

• Binding Poses and Energies CalculationKNIME Hub
• Cocrystallized ligand redocking 1-2KNIME Hub
• Cocrystallized ligand redocking 2KNIME Hub
• Docking 1KNIME Hub
• Docking 1KNIME Hub
• Show all 16 workflows

Links

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Developers