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Table 2 The lowest lRMSD to the known native structure over conformations in the output ensemble Ω α is reported for the 15 target protein systems.

From: A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction

  Native PDB ID Avg(Min) Lowest lRMSD (Å)
   EA - AMW MEA - AMW MEA - Rosetta FeLTr ItFix EdaFold
1 1bq9 5.5(5.1) 5.2(4.8) 4.1(2.9) 6.3(5.6) N/A 2.0
2 1dtdB 8.1(7.3) 7.0(6.8) 6.5(4.7) 7.7(7.6) 6.5 N/A
3 1isuA 7.6(7.2) 6.6(6.4) 7.3(7.2) 6.8(6.7) 6.5 N/A
4 1c8cA 8.6(8.5) 7.3(6.9) 7.1(6.1) 6.5(6.0) 3.7 N/A
5 1sap 7.9(7.2) 6.7(6.1) 5.4(5.0) 7.1(6.5) 4.6 N/A
6 1hz6A 6.5(5.3) 6.1(6.0) 3.4(3.1) 6.6(6.6) 3.8 N/A
7 1wapA 9.2(8.7) 7.7(6.9) 8.1(8.0) 7.8(7.3) 8.0 N/A
8 1fwp 7.6(7.2) 6.8(6.6) 6.6(5.2) 6.8(6.4) 8.1 N/A
9 1ail 4.9(4.1) 3.3(3.2) 5.5(5.1) 4.7(4.5) 5.4 N/A
10 1dtjA 8.1(7.7) 5.6(4.9) 5.4(4.5) 9.2(8.4) N/A 2.7
11 1aoy 7.0(6.3) 5.4(5.1) 6.0(5.4) 5.1(4.6) 5.7 N/A
12 2ci2 6.9(6.5) 5.3(5.2) 4.7(3.8) 8.8(7.25) N/A 3.2
13 1cc5 7.3(6.5) 5.7(5.5) 6.7(6.3) 6.4(6.2) 6.5 N/A
14 1tig 8.3(7.8) 6.5(6.3) 3.9(2.6) 10.8(10.4) N/A 3.4
15 2ezk 6.0(4.9) 4.8(4.4) 5.1(4.7) 6.4(6.0) 5.5 N/A
  1. The average and minimum lowest lRMSD obtained over 3 independent runs is shown for the Evolutionary Algorithm (EA) in column 3 and the Memetic EA (MEA) in column 4. Both of these columns are from results run with the AMW energy function. Column 5 evaluates the same MEA algorithm as column 4, but with the Rosetta energy function instead of AMW. Column 6 shows values obtained by the MMC-based FeLTr decoy sampling method [49], column 7 shows lowest lRMSDs published the Sosnick lab for the ItFix method [27], and column 8 shows lowest lRMSDs published for the EdaFold method on a subset of proteins [62].