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