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Table 3 Rosetta multi-objective reduction technique.

From: Rapid sampling of local minima in protein energy surface and effective reduction through a multi-objective filter

Rosetta Energy Function
  Native PDB Id Ω PF reduction Minimum lRMSD (Å)
   ( r = | Ω PF |/| Ω | ) Ω Ω TE ( r ) Ω PF Ω TE (5%) Ω TE (10%) Ω PC (5%) Ω PC (10%)
1 1dtdB 1% 6.7 10.8 9.1 10.6 10.2 10.2 8.6
2 1isuA 2% 6.5 8.9 8.6 8.9 8.6 8.0 7.5
3 1c8cA 2% 5.6 7.9 7.1 7.8 7.0 7.1 6.8
4 1sap 3% 6.1 7.4 7.1 7.4 6.8 6.8 6.6
5 1hz6A 3% 2.5 2.8 2.8 2.8 2.6 2.7 2.6
6 1wapA 1% 7.4 8.8 8.8 8.5 8.5 8.8 8.1
7 1fwp 3% 6.1 7.2 7.0 7.1 7.1 7.2 6.9
8 1ail > 1% 4.8 8.2 6.2 7.6 7.5 7.5 6.9
9 1aoy 2% 6.2 10.1 9.1 9.2 9.2 9.3 9.2
10 1cc5 1% 5.0 6.3 6.3 5.7 5.7 5.5 5.4
11 2ezk 1% 3.9 9.1 6.2 5.2 5.1 5.1 4.9
12 1hhp 3% 10.8 13.9 12.6 13.9 13.6 13.0 12.9
13 2hg6 2% 10.6 12.2 11.5 12.0 12.0 12.0 11.7
14 3gwl 1% 7.1 8.9 8.5 8.7 8.4 8.0 7.8
15 2h5nD 1% 8.9 13.0 10.4 12.3 12.1 12.2 11.4
  1. The minimum lRMSD to the native structure retained by each of the proposed multi-objective ensemble reduction techniques is given for the Ω generated with the Rosetta energy function. Column 3 gives the size of the Pareto front as a percentage of the size of Ω. Column 4 gives the minimum lRMSD to the native structure of any conformation in the Ω. Columns 5 and 6 give minimum lRMSD retained by Ω TE (r)and Ω PF , respectively, where r is the corresponding value from Column 3. Columns 7-10 compare the minimum lRMSD retained by Ω TE (n)and Ω PC (n)for thresholds of n = 5% and n = 10%.