Induced Fit Docking

Set up a sequence of jobs in which ligands are docked with Glide, then Prime Refinement is used to allow the receptor to relax, and the ligands are redocked into the relaxed receptor with Glide.

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 "Induced Fit 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: IFD
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 output of IFD

Log output of IFD

IFD StdOutErr View

Std output/error of IFD

Workflows

• Induced-fit docking 1KNIME Hub
• Induced-fit docking 1KNIME Hub
• Induced-fit docking 1-2KNIME Hub
• Induced-fit docking 1-2KNIME Hub

Links

• No links available

Developers