Covalent Docking

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

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.

Views

Log file output

Log file output

StdOutErr View

Std output/error

Workflows

• Covalent dockingKNIME Hub
• Covalent dockingKNIME Hub

Links

• No links available

Developers