Access method efficiency The efficiency of the SProt access method was measured for different weights of the modifier and for different numbers of requested nearest neighbors. All the 108 queries of the ProtDex2 dataset were utilized and the average values are presented. The efficiency is expressed both in terms of the relative (according to sequential scan) number of protein structure pairs being compared (A) and in terms of the relative (according to sequential scan) computation time (B). Figure (B) also includes the absolute time which was measured on a machine containing an Intel Xeon E7540 2.00GHz processor. The sequential scan takes 39.4 minutes on average. Vertical dashed lines denote minimal, average and maximal size of the query families in the dataset.