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Covalent Docking

Schrödinger extension for KNIME Workbench version 20.4.144.202011111133 by Schrödinger

Dock a set of ligands to a receptor, in which the ligands form a covalent bond to a receptor residue or site by a specified type of reaction (such as a Michael addition). The ligands must all contain the reactive group, which is specified by a SMARTS pattern.

Backend implementation

$SCHRODINGER/covalent_docking

Options

Column containing receptor input
Select the column containing the receptor
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 "Covalent Docking" Python panel for configuration.
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: CovalentDocking
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
Receptor or Complex structures in Maestro format
Icon
Ligands in Maestro format

Output Ports

Icon
Complex structures in Maestro format

Views

Log file output
Log file output
StdOutErr View
Std output/error

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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