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MoSS MCSS Molecule Similarity

KNIME MoSS node version 4.3.0.v202011191214 by KNIME AG, Zurich, Switzerland

This nodes computes similarities between pairs of molecules by taking the size of their MCSS as a measure for similarity (the bigger the MCSS the more similar the molecules are). For computing the MCSS, the substructure miner MoSS is used. Since the computation of a MCSS is a complex problem and can take quite a lot of time you can set a timeout after which the computation of a single MCSS between two molecule is aborted. In this case the distance between the two molecules will be the biggest common substructure found so far.
This node may use quite a lot of memory thus if you run into problems try to increase the available heap size for KNIME in the knime.ini.


Molecule column
Select the column containing the SDF molecules here
Chunk size
Specify the number of rows to be considered at once. Increasing this number will speed up runtime but may require more memory to be used. This value has no impact on the outcome, it only influences runtime.
Certain molecule pairs require a lot of time to compute their MCSS. You can set a timeout here after which the search is stopped and the currently biggest common substructure is used as the MCSS.

Input Ports

Input table with at least a molecule column

Output Ports

Input table with an additional column containing the computed distances between the molecules

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install KNIME Chemistry Add-Ons from the following update site:


A zipped version of the software site can be downloaded here.

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