Table 4 The average accuracies and success rates of MODPEP, PEP-FOLD3, Balloon, and RDKit in reproducing protein-bound conformations for the peptides with different lengths when an ensemble of 200 conformations were considered for each peptide
From: Efficient conformational ensemble generation of protein-bound peptides
Peptide | cRMSD (Ă…) | Success rate (%) | |||||||
|---|---|---|---|---|---|---|---|---|---|
Length | Number | MODPEP | PEP-FOLD3 | Balloon | RDkit | MODPEP | PEP-FOLD3 | Balloon | RDkit |
3 | 11 | 0.04 | 0.00 | 0.27 | 0.07 | 100 | 0.0 | 100 | 100 |
4 | 43 | 0.21 | 0.00 | 0.53 | 0.28 | 100 | 0.0 | 100 | 100 |
5 | 32 | 0.45 | 2.00 | 0.96 | 0.57 | 100 | 31.2 | 96.9 | 96.9 |
6 | 47 | 0.65 | 2.18 | 1.47 | 1.03 | 97.9 | 31.9 | 61.7 | 87.2 |
7 | 49 | 0.96 | 2.88 | 2.21 | 1.21 | 100 | 24.5 | 30.6 | 79.6 |
8 | 60 | 1.29 | 2.94 | 2.70 | 1.75 | 95.0 | 25.0 | 26.7 | 73.3 |
9 | 138 | 1.56 | 3.32 | 3.34 | 1.82 | 97.8 | 15.2 | 8.0 | 79.7 |
10 | 60 | 1.67 | 2.80 | 3.61 | 2.20 | 96.7 | 30.0 | 6.7 | 61.7 |
11 | 62 | 2.04 | 3.17 | 3.78 | 2.81 | 77.4 | 25.8 | 4.8 | 43.5 |
12 | 40 | 2.09 | 2.48 | 3.57 | 3.22 | 52.5 | 47.5 | 20.0 | 12.5 |
13 | 50 | 2.29 | 3.40 | 4.53 | 3.56 | 58.0 | 36.0 | 6.0 | 32.0 |
14 | 45 | 2.64 | 3.66 | 5.13 | 3.67 | 48.9 | 37.8 | 2.2 | 26.7 |
15 | 33 | 2.58 | 3.71 | 5.59 | 3.99 | 36.4 | 30.3 | 0.0 | 18.2 |
16 | 29 | 2.66 | 3.39 | 5.49 | 4.61 | 41.4 | 34.5 | 0.0 | 3.4 |
17 | 12 | 2.56 | 3.50 | 6.33 | 5.41 | 50.0 | 50.0 | 0.0 | 0.0 |
18 | 25 | 2.93 | 3.61 | 5.73 | 5.78 | 44.0 | 32.0 | 0.0 | 4.0 |
19 | 21 | 2.38 | 3.05 | 6.24 | 5.49 | 61.9 | 52.4 | 0.0 | 4.8 |
20 | 16 | 3.14 | 4.51 | 6.78 | 6.37 | 50.0 | 18.8 | 0.0 | 0.0 |
21 | 21 | 3.05 | 3.09 | 5.24 | 8.99 | 42.9 | 52.4 | 0.0 | 0.0 |
22 | 21 | 2.43 | 2.92 | 6.09 | 7.46 | 61.9 | 47.6 | 0.0 | 4.8 |
23 | 10 | 3.01 | 5.05 | 7.20 | 0.00 | 50.0 | 10.0 | 0.0 | 0.0 |
24 | 17 | 3.11 | 4.12 | 7.07 | 4.41 | 47.1 | 41.2 | 0.0 | 0.0 |
25 | 15 | 2.71 | 4.41 | 7.48 | 0.00 | 60.0 | 33.3 | 0.0 | 0.0 |
26 | 10 | 2.77 | 3.68 | 7.84 | 0.00 | 40.0 | 40.0 | 0.0 | 0.0 |
27 | 10 | 3.95 | 5.33 | 8.53 | 0.00 | 30.0 | 30.0 | 0.0 | 0.0 |
28 | 14 | 3.05 | 4.57 | 7.89 | 6.15 | 42.9 | 28.6 | 0.0 | 0.0 |
29 | 14 | 4.24 | 5.47 | 7.92 | 9.77 | 21.4 | 28.6 | 0.0 | 0.0 |
30 | 5 | 2.72 | 6.38 | 8.32 | 0.00 | 60.0 | 0.0 | 0.0 | 0.0 |
All | 910 | 1.90 | 3.28 | 4.04 | 2.63 | 74.3 | 30.1 | 19.2 | 46.8 |