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Protein Structure Alignment

Schrödinger extension for KNIME Workbench version 21.1.156.202102141445 by Schrödinger

Protein Structure Alignment uses SKA to align protein structures to a reference structure. The reference structure provides the frame of reference to which all other structures are aligned.

Backend implementation

utilities/structalign
The script structalign_utility.py is used to implement this node.

Options

Column containing reference structure
Select column in the input data table containing the reference structure
Column containing mobile structures
Select column in the input data table containing the mobile structures
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

Force alignment
Align each mobile structure separately to the reference structure, i.e. generate the optimal alignment for every pair of structures.
ASL
ASL for the substructures to align.
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: PSA
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 from command line, just specify the option_name and the value as _off_ through the flow variable.

Input Ports

Icon
Reference Structure in Maestro or PDB format
Icon
Mobile Structures in Maestro or PDB format

Output Ports

Icon
Aligned Structures in Maestro or PDB format

Views

Standard output/error
Standard 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 4.3

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Developers

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