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Glide Ligand Docking

Schrödinger extension for KNIME Workbench version 20.3.139.202008121324 by Schrödinger

Glide ligand docking jobs require a set of previously calculated receptor grids and one or more ligand structures. Preparation of the ligands before docking is strongly recommended. LigPrep or MacroModel can be used to prepare ligands. If a correct Lewis structure cannot be generated for a ligand, it will be skipped by the docking job.

Backend implementation

$SCHRODINGER/glide

Options

Column containing receptor input
Select the column containing Glide grid
Column containing ligands to be docked
Select the column containing the ligands to be docked
Output Column Structure
Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Settings...
On clicking "Settings" button, this node brings up the "Glide Ligand Docking" Python panel for configuration.
Read Maestro Settings...
On clicking "Read Maestro Settings" button, this node brings up a directory browser. Browse to a 'Glide Ligand Docking' job diretcory written by Maestro and click OK. The "Glide Ligand Docking" Python panel will now be opened by loading the settings read from the job directory.
Parameter flow variables
Flow variable prefix keyword: GlideDockingInput
Use this prefix to control the Glide docking keywords in the input file (.in)
For example,
Flow variable name: GlideDockingInput-PRECISION
Flow variable value: XP

Flow variable prefix keyword: GlideDocking
Any valid command line option for this node can be specified through flow variables. Only String variables are accepted.
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
Glide Grid
Icon
Ligands in Maestro, Sd or Mol2 format

Output Ports

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Pose Viewer in Maestro or Sd format (i.e Receptor and docked ligands or only ligands)

Views

Log file
Log output
Subjobs log file
Subjobs log output

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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