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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 (Ã…)

  

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].
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BMC Structural Biology

ISSN: 1472-6807

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