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A tool/algorithm for calculating the largest common subgraph between sets of molecules?

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I would like to calculate the largest common subgraph from a set of molecules. Any pointers to published algorithms or open source tools?

Many thanks,

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4 answers


mikhail-rybalkin [ Editor ] from Российская Федерация

Hello Hans,

Our cheminformatics toolkit Indigo has such functionality. You can download a command-line tool indigo-deco:

Or you can write a program (in Python, C#, Java, or C) using our library. You can find an example here:

Or you can install KNIME and install Indigo Nodes for it, which contain Maximum Common Scaffold node.

Best regards,

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rajarshi guha [ Editor ] from Hartford, United States of America

NN comments

Be aware that finding the MCSS between two structures is a different problem from finding them in a larger set. The set MCSS is not necessarily the same, or a substructure of, as any structure pair MCSS from the set. There are papers/published algorithms which get this wrong, and assume that you can start with a structure pair MCSS, and then use that iteratively to shave off more atoms by comparing it to the other structures. That is a faulty approach (though, due to the nature of chemical structures, it still is quite often successful).

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