Head to head comparison of MCS jobs processed by SMSD and CDK-MCS. The similarity score frequencies (left axis) between each pair (colored boxes) of MCS solutions derived by the CDKMCS and the SMSD algorithm were sorted into bins ranging from 0 to 1 increasing in 0.01 increments. The cumulative percentage of the overall dataset for each bin is also shown (curves and right axis). Data shown in blue correspond to results from the SMSD algorithm while those in mauve correspond to CDKMCS. Data shown in yellow correspond to all the jobs that ran successfully by SMSD (includes 24 jobs which failed to run by CDKMCS). It is clear from the graph that the reported frequency of the SMSD similarity is almost similar to the CDKMCS similarity between the molecules. However the overall similarity between SMSD and CDKMCS is different because SMSD was able to process higher number of jobs than the latter. A good cut-off Tanimoto similarity score for reporting significant matches seems to be above 0.77 (at 99.9 percentile of the curve) for MCS based searches (indicated by the rightmost set of dashed lines).