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Docking (FlexX)

This node takes a protein and a reference molecule to define a binding site. Molecules from the input table are docked with FlexX into this binding site. Alternatively, if a template molecule is provided, those molecules are overlayed onto the template based on the maximum common substructure (MCS) and scored using the FlexX-scoring function. The solutions with the best scores are written to the output table. Molecules that cannot be docked for whatever reason, are written to the error table.

You may also define your docking with the SeeSAR Interactive node. Besides the binding site you will be able to define pharmacophore constraints for your docking results.

FlexX has to be licensed separately, see http://www.biosolveit.de/FlexX/ for more details.

Options

Library column

Name of the column containing the molecules that should be docked. Allowed formats are sdf or mol2. 3d coordinates are required.

Reference ligand column

Name of the column containing a reference molecule that is used to define the binding site. Allowed formats are sdf or mol2. 3d coordinates are required.

Protein column

Name of the column containing the protein in pdb format.

Template column

Name of the column containing a template molecule that is used for an MCS-based alignment. Allowed formats are sdf or mol2. 3d coordinates are required.

Perform covalent docking

To perform covalent docking

A SeeSAR project has to be provided with a binding site prepared to perform covalent docking and
this option has to be checked

If this option is unchecked although a covalent-docking-ready binding site is provided in the project, a standard or template docking will be performed.

Maximum number of poses

Choose the maximum number of poses per input molecule.

Append all data columns of the library table

Select this if you want to append all data columns of your input table to the output table.

Keep debug files and show the log after the run

This setting keeps all temporary files and opens an editor to show the output of the external program. This setting is very helpful for debugging.

Input Ports

: Library: Input table with molecules in sdf or mol2 format with 3d coordinates.
: Reference Ligand: Input table with a binding site defining molecule in sdf or mol2 format with 3d coordinates. In case of multiple entries, only the first one will be taken.
: PDB: Input table with a protein column in pdb format.
: Template Pose: Input table with a template molecule in sdf or mol2 format with 3d coordinates. In case of multiple entries, only the first one will be taken.
: SeeSAR Project: Reference ligand and protein will be ignored, if a project is available.

Output Ports

: Results: The FlexX docking poses in sdf format.
: Errors: Rows of the incoming table containing molecules which could not be docked for any reason.

Popular Predecessors

Generate 3D Coordinates12 %
Mol2 Reader8 %
PDB Loader6 %
FXX Data Extractor6 %
SDF Reader4 %
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Installation

To use this node in KNIME, install the extension BioSolveIT FlexX for Knime from the below update site following our NodePit Product and Node Installation Guide:

v5.2

Plugin provider: BioSolveIT GmbH

Plugin version: 2.29.3.202309291626

On NodePit since: 2023-12-06

Last update: 2024-11-20

KNIME versions: From v3.6 to v5.2

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