Figure 3.
Contribution of Strategies 1 and 2 on TM1112. The number of Cα 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 Cα RMSD. The contribution from the upper bounds via the reference decoys can be completely accounted for by rRMSD, while Cα 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 Cα 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 Cα 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.