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Molecule Aligner (FlexS)

BioSolveIT FlexS for Knime version by BioSolveIT GmbH

This node performs FlexS 3d alignments. The approach used here is to have a query molecule which is used as a so-called reference, and a molecule data stream (library) at the input ports. The library molecules will be aligned onto the reference molecule and the aligned conformations will be sent to the output port.

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


Library column
Name of the column containing the molecules that should be aligned. Allowed formats are sdf or mol2. 3d coordinates are required.
Reference molecule column
Name of the column containing the reference molecule. Allowed formats are sdf or mol2. 3d coordinates are required.
Number of alignments
Specify the maximum number of generated aligned molecules 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 Molecule: Input table containing the reference molecule with 3d coordinates.

Output Ports

Aligned Molecules: The FlexS alignment results in sdf format.
Errors: The molecules that couldn't be processed for any reason. This table contains a copy of the erroneous input table rows.


To use this node in KNIME, install BioSolveIT FlexS for Knime from the following update site:


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