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Table 4 The performance of different models on 16 peptides in ModPep16 dataset. All models were subjected to 100 ps molecular dynamics simulations in vacuum environment

From: PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues

  

ab initio model

PEPstrMOD

DSSP model

PDB ID

La

CA-RMSD

B-RMSD

CA-RMSD

B-RMSD

CA-RMSD

B-RMSD

 1fevA

15

5.25

5.12

2.20

2.57

1.82

1.78

 1rbdS

15

5.16

5.07

4.86

4.93

5.64

5.08

 1tkqB

15

6.46

5.51

6.11

5.95

5.65

5.46

 1z3lS

15

5.93

5.45

4.28

3.33

4.78

4.65

 1z3mS

15

5.57

5.49

4.81

4.94

3.67

1.73

 1z3pS

15

3.39

3.61

4.16

3.90

6.72

6.62

 2ap8A

20

4.72

4.78

1.37

0.90

1.17

0.91

 2dprA

21

5.60

5.41

1.65

1.52

0.92

0.90

 2fx8P

12

4.17

4.15

4.76

4.77

0.88

0.78

 2k7lB

19

5.99

6.04

6.60

6.44

0.90

0.98

 2rlnS

15

4.16

4.00

6.07

4.69

6.69

2.55

 3cmhA

15

5.21

5.26

4.83

4.75

4.59

4.41

 3kmzC

19

5.32

4.83

1.69

1.24

2.65

2.77

 3zs2D

25

7.23

7.33

5.23

4.85

5.86

5.70

 4lkaB

12

4.65

3.93

4.39

4.17

3.25

2.73

 6cmhA

21

8.81

8.71

5.96

5.80

5.56

3.87

Average

 

5.48

5.29

4.31

4.05

3.80

3.18

  1. CA-RMSD C-alpha Root Mean Square Deviation, B-RMSD Backbone Root Mean Square Deviation
  2. aLength of the peptide