Figure 3.

MASTER search time as a function of the number of disjoint segments in the query and the number of matches (determined by the RMSD cutoff used). Each dot corresponds to a single query–RMSD cutoff combination, with those taking more than a minute to search marked as squares. Queries with different numbers of segments are differentiated by color for clarity. The search slows down substantially only when the specified RMSD cutoff corresponds to a very large number of matches, and mostly with complex queries. Inset shows the same plot with the Z-axis in logarithmic scale.