Figure 4. Comparison between ProSMoS and Dali. The red curve is the average precision of ProSMoS searches of eight common structure patterns. The dark blue curve is the average recall. The x-axis is the Dali Z-score used to deﬁne ‘true’ matches. structure patterns are available at: http://prodata.swmed. edu/ProSMoS/prepattern.html Comparison between ProSMoS and Dali ProSMoS ﬁnd structures matching a user-deﬁned pattern. DALI (6) ﬁnds structures sharing contact similarity with the query. Although these two approaches are quite diﬀerent, comparison of the two programs is instructive because the majority of structural biologists are well-familiar with DALI. We compared ProSMoS and DALI on eight common structure patterns (http:// prodata.swmed.edu/ProSMoS/comparetest/) in terms of precision = TP/(TP + FP) and recall = TP/(TP + FN), where TP, FP and FN are true positives, false positives and false negatives, respectively. Experiments were done with varying DALI Z-score cutoﬀs on SCOP40 database (9479 domains). Coordinates of the ﬁrst motif found by ProSMoS were used as a DALI query. Structures found by DALI above the given cutoﬀ (Z-score higher than the cutoﬀ) were considered ‘true’, below the cutoﬀ were con- sidered ‘false’. DALI found 1408 domains (15% of total domains) in all eight families above Z-score of 2. ProsMoS found motifs in 2947 domains (31% of total domains). The results, averaged for eight patterns, are shown in Figure 4. Precision and recall values are about the same for DALI Z-score cutoﬀ 4. When DALI Z-score is lower, many DALI hits do not have the pattern and similarity between structures resides elsewhere, for instance in a long a-helix, thus ProSMoS recall is low. 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