Benchmarks: Lindahls and Fischer et al.

Fischer et als benchmark set consists of 68 target sequences and 301 templates. RAPTOR ranks 56 pairs out of 68 pairs as top 1, achieving about 82% prediction rate. The fold recognition performance of RAPTOR was further tested on Lindahls benchmark set consisting of 976 protein sequences. By threading them all against all, there are 976 975 threading pairs. We measured RAPTORs performance in three similarity levels: fold, superfamily and family. Results are shown in Table 1 (data of other methods are taken from Shi et als paper). Prediction correctness is assessed based on the SCOP classification.

Table 1. The performance of RAPTOR at three different similarity levels

As shown in Table 1, RAPTOR performs better than other methods at all similarity levels (especially the fold level). At the family level, RAPTORs recognition performance is comparable to that of FUGUE, the best method for family and superfamily level other than RAPTOR. We may conclude that a strict treatment of pairwise interactions is necessary for fold and superfamily level recognition. For the family level, sequence (or profile) alignment could attain satisfactory results.