I would like to calculate the largest common subgraph from a set of molecules. Any pointers to published algorithms or open source tools?
Mikhail Rybalkin [ Editor ] from Российская Федерация
Our cheminformatics toolkit Indigo has such functionality. You can download a command-line tool indigo-deco: http://ggasoftware.com/download/indigo_next
Or you can write a program (in Python, C#, Java, or C) using our library. You can find an example here: http://ggasoftware.com/opensource/indigo/api#r-group-deconvolution
Or you can install KNIME and install Indigo Nodes for it, which contain Maximum Common Scaffold node.