MCS Scaffold Finder

This node finds the maximum common scaffold (MCS) of an arbitrary amount of the input molecules. In case of multiple MCS, they are all written to the output table

Supported types:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI

The node is based on the Indigo cheminformatics toolkit.


Molecule column
The column that contains molecule structures.
New column with scaffolds
Name for the new column that contains the found scaffold(s).
Try exact method
Try to find the exact MCS (may take a lot of time on some complex structures, which gives the reason for the iterations limit parameter.
Maximum number of iterations for exact method
If this limit is reached without exact MCS found, the node falls back to the approximate method. Zero value of this parameter means no limit (i.e. never fall back to the approximate method).
Number of iterations for approximate method
The approximate method is guaranteed to terminate after this number of iterations.
Input type
Treat input as: a molecule.
Treat X as pseudoatom
Treat the "X" atoms in Molfiles as pseudoatoms, not as "any halogen" query atoms.
Ignore stereochemistry errors
Ignore incorrectly specified stereochemistry on input structures, rather than sending the structures with stereochemistry errors to the "invalid molecules" table.

Input Ports

Table containing molecules

Output Ports

Query molecules that are the found maximum common scaffolds.


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