Performances among different structural classes and proteins with incomplete structures. The average fallouts after the retrieval of 80 proteins were calculated. Because fallout is a measure of the false positive rate, these data demonstrate that the performances of SARST are fairly even (i.e. no obvious bias) among the four major classes as compared to those of BLAST. The fallouts of SARST are generally lower than YAKUSA  and 3D-BLAST , both of which are protein structural similarity search tools with linear encoding methodologies. When tested with query proteins having incomplete local backbone structures, SARST outperforms other linear encoding methods and CE. The query proteins used in this experiment was set by Aung and Tan ; the subset of incomplete structures and the extent of incompleteness are listed in the supplementary materials [see Additional file 5].