Figure 4.

A test of psi-blast for automated fold assignment. Using psi-blast with the SwissProt sequence database, we used 3,285 sequences from our training set to generate an exhaustive set of 10,784,656 (3,285 × 3,284) nonself sequence–sequence assignment pairs. Using binary hypothesis testing, we divided the resulting set of scores into two cases. For the set of correct matches (dashed line), the actual structures for the two sequences were similar as determined by a dali Z-score greater than or equal to 2. The set of incorrect matches is also shown (solid line). The reduced separation of these cases compared with the results for SDP shown in Fig. 1A implies that confidence intervals may be more difficult to generate by using psi-blast.