MoSS MCSS Molecule Similarity

This node computes similarities between pairs of molecules by taking the size of their MCSS as a measure of 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 an 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 molecules 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, so if you run into problems, try to increase the available heap size for KNIME in the knime.ini.

Options

Molecule column

Select the column containing the molecules or structures 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.

Timeout (ms)

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. The timeout is specified in milliseconds.

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Workflows

• 05_Score_Erosion_for_Multi_Objective_OptimizationKNIME Hub
• BindingDB_FMCT-Fingerprint+MCSKNIME Hub
• BindingDB_FMCT-MCSKNIME Hub
• DrugRepurposingPipeline_OpenTargetsKNIME Hub

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