Ligand Alignment

Align a set of ligand structures flexibly with torsional variation, using the best available method
Backend implementation
One of the below:
$SCHRODINGER/utilities/align_ligands
$SCHRODINGER/utilities/phase_align_core
$SCHRODINGER/utilities/flex_align

Options

Column containing reference structure

Select the column containing reference structure. This port is optional. If not connected, the first structure in the ligands will be used as reference. If "Choose automatically" is selected in the panel, and if a reference structure is specified, then it wil be ignored.

Column containing ligands to be aligned

Select the column containing the ligands to be aligned

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

Include reference in output

If ON, include the reference strucutre (if specified in Reference port) in the output. Default is OFF.

Settings...

On clicking "Settings" button, this node brings up the "Ligand Alignment" 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: LigandAlignment
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

Log output

Workflows

• Alignment and rescoringKNIME Hub
• Ligand alignment 1KNIME Hub
• Ligand alignment 1-2KNIME Hub
• Ligand alignment with a cocrystallized referenceKNIME Hub
• Macrocycle strain EnergyKNIME Hub

Links

• No links available

Developers