Figure 3

Contribution of Strategies 1 and 2 on TM1112. The number of C _α RMSD computations avoided (percentage over 9999 × 9998 computations) due to each of the cases considered, at different threshold values. For Case 2, the upper bounds are used for condition evaluation prior to the actual C _α RMSD. The contribution from the upper bounds via the reference decoys can be completely accounted for by rRMSD, while C _α RMSD evaluations contributed insignificantly. Only the contribution from rRMSD (label "Case 2 rRMSD_U") is shown. For Case 3, the lower bounds are used for condition evaluation prior to the actual C _α RMSD. While the contributions from both kinds of lower bounds overlapped (label "Case 3_Ref_L or Sig_L"), there were contributions entirely due to evaluations using the signature (label "Case 3 Sig_L only") as well as the reference decoys (label "Case 3 Ref_L only"). The contribution from evaluating the actual C _α RMSD was highly significant as well (label "Case 3"). In evaluating individual decoys, the upper bound obtained from rRMSD was highly effective at high thresholds (label "Accept decoy, rRMSD_U"). The lower bounds from the reference decoys demonstrated noticeable effects (label "Reject decoy, Ref_L"). Other contributions were insignificant.