If you are looking for quick exact MCS calculations on molecules, then look no further!
The CheMCS (or Chemical Maximum Common Subgraph) tools were developed from my PhD project with Professor Peter Willett and Dr John Holliday at the University of Sheffield. Of main note with the tools presented on this site, is the ability to quickly calculate the MCS on several molecules quickly, whilst yielding more geometrically sensible MCSs which show a more intuitive similarity.
This has been developed as a companion tool for the CheMCS GUI. It has been designed to be used for larger scale cases, such as similarity searching databases and virtual screening.
Of note, is not currently supporting parallel processing. This, will be added in the near future.