Retrieval errors The retrieval errors of the SProt access method were 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 errors are described as the percentage of protein structures included in the sequential scan result and missing in the result of the SProt access method. In the first case (A), the whole result of sequence scan is considered and the retrieval error E is measured. In the other cases, only subsets of the result sharing the same SCOP family (B), superfamily (C) or fold (D) with the query structure are taken into account, leading to different SCOP retrieval errors. An error 0% means that none of the considered structures were missing, and conversely, an error 100% means that all considered structures were missing. Vertical dashed lines denote minimal, average and maximal size of query families in the dataset.