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Finding the maximum common substructure (MCS) among molecules has many applications in the field of cheminformatics. It can be used in automated reaction mapping and molecule alignment, and it is also a popular measure of similarity, just to name a few. However, the complexity of the problem makes finding the exact MCS of two molecules too time-consuming for most use cases. At ChemAxon, we employ approximation algorithms in MCS search, but building one which is both practically fast and accurate is still a challenge. To meet the increasing demands on effective MCS search, we have taken our previous approach and applied different heuristics to further improve its speed and accuracy. The results are very promising, both in large-scale tests involving thousands of different compounds, and in application-specific cases.