Evaluation of residue-residue contact predictions in CASP9

Abstract

This work presents the results of the assessment of the intramolecular residue-residue contact predictions submitted to CASP9. The methodology for the assessment does not differ from that used in previous CASPs, with two basic evaluation measures being the precision in recognizing contacts and the difference between the distribution of distances in the subset of predicted contact pairs versus all pairs of residues in the structure. The emphasis is placed on the prediction of long-range contacts (i.e., contacts between residues separated by at least 24 residues along sequence) in target proteins that cannot be easily modeled by homology. Although there is considerable activity in the field, the current analysis reports no discernable progress since CASP8.

Figure 1

Number of targets evaluated for each group using the L/10, L/5 and Top-5 lists of contacts.

Figure 2

Average value of the accuracy (Acc) obtained by the participating groups for each of the targets using the L/10, L/5 and Top-5 lists of contacts.

Figure 3

Acc (a), Xd (b) and Z-score (c) values for the participating groups.

Figure 4

Comparison of the results obtained by the best twelve predictors in CASP8 and CASP9. The twelve groups were selected based on the Acc score.