Figure 3

CASP9 prediction performance. (A) CASP prediction performance as measured by accuracy for the L/10 contacts (L = length of target sequence) with the highest predicted scores, as a function of the number of sequences in the sequence alignment. Red, RMRCM prediction performance; black, best prediction performance among all CASP participants; blue, average prediction performance among all CASP participants. For two out of the four cases with the highest number of sequences, RMRCM performance is better than that of any of the CASP participants; for these two cases, labels are added to identify the CASP targets. (B) Protein structure for target T0604-D3 in cartoon representation, together with the 20 top-ranked predicted contacts in spacefill (20 corresponds to L/10 for this protein). Identical colors for the residues indicate pairs of residues for which a contact was predicted. Out of those 20 residues, 14 are contacts according to the CASP criteria, and most of the others are relatively close to each other as well (within 15 Å).