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Table 2 AMW multi-objective reduction technique.

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

AMW Energy Function

 

Native PDB Id

Ω PF reduction

Minimum lRMSD (Ã…)

  

( r = | Ω PF |/| Ω | )

Ω

Ω TE ( r )

Ω PF

Ω TE (5%)

Ω TE (10%)

Ω PC (5%)

Ω PC (10%)

1

1dtdB

4%

7.2

7.9

7.7

7.9

7.7

7.7

7.7

2

1isuA

7%

6.0

6.2

6.5

6.4

6.2

6.2

6.2

3

1c8cA

4%

7.4

7.5

7.5

7.5

7.5

7.5

7.5

4

1sap

2%

6.5

7.6

7.5

7.4

7.2

7.4

7.2

5

1hz6A

2%

5.9

6.7

6.3

6.7

6.7

6.7

6.6

6

1wapA

2%

7.7

8.7

8.7

8.7

8.7

8.7

8.7

7

1fwp

7%

6.4

8.1

7.3

8.1

8.1

8.1

8.1

8

1ail

2%

3.4

6.8

5.9

5.8

4.2

4.7

4.4

9

1aoy

6%

5.7

6.9

6.6

6.9

6.5

6.8

6.5

10

1cc5

7%

5.6

8.6

7.0

8.7

8.6

8.6

8.1

11

2ezk

3%

4.4

8.0

7.3

7.7

7.1

7.2

7.1

12

1hhp

1%

10.7

12.0

12.0

11.6

11.6

11.6

10.8

13

2hg6

6%

8.6

10.8

10.5

11.6

10.8

10.9

10.8

14

3gwl

5%

4.2

4.7

5.2

4.7

4.7

4.7

4.7

15

2h5nD

7%

7.9

10.7

10.0

10.8

10.4

10.4

10.4

  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 AMW 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%.