Recently we have been working on extending and cleaning the SMSD command line tool. One of the priority requests from the SMSD users was to be able to obtain MCS between N-molecules. Thanks to Gilleain who has been instrumental in cleaning the code and providing a good visual output to the searches. He has implemented a circular layout for the MCS search between N-molecules. This looks cleaner and visually appealing to the users.
You can download SMSDcmd-3.0.jar from our website. Try the following command line option for obtaining MCS between N-molecules
> java -jar SMSDcmd-3.0.jar -T SDF -N Data/arom.sdf -g -b
You can download/clone the arom.sdf.
The result would look something like this