Table 3 The success rates of our MODPEP method in reproducing protein-bound conformations for the peptides with different lengths when various ensemble sizes were considered
From: Efficient conformational ensemble generation of protein-bound peptides
Peptide | Success rate (%) | ||||||||
|---|---|---|---|---|---|---|---|---|---|
Length | Number | 50 | 100 | 150 | 200 | 250 | 300 | 500 | 1000 |
3 | 11 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
4 | 43 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
5 | 32 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
6 | 47 | 97.9 | 97.9 | 97.9 | 97.9 | 97.9 | 97.9 | 97.9 | 97.9 |
7 | 49 | 98.0 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
8 | 60 | 83.3 | 91.7 | 93.3 | 95.0 | 96.7 | 96.7 | 96.7 | 96.7 |
9 | 138 | 75.4 | 92.8 | 96.4 | 97.8 | 98.6 | 98.6 | 98.6 | 99.3 |
10 | 60 | 71.7 | 81.7 | 90.0 | 96.7 | 96.7 | 98.3 | 98.3 | 98.3 |
11 | 62 | 45.2 | 58.1 | 69.4 | 77.4 | 79.0 | 80.6 | 82.3 | 90.3 |
12 | 40 | 37.5 | 42.5 | 47.5 | 52.5 | 55.0 | 57.5 | 80.0 | 92.5 |
13 | 50 | 38.0 | 48.0 | 50.0 | 58.0 | 62.0 | 64.0 | 74.0 | 80.0 |
14 | 45 | 31.1 | 33.3 | 42.2 | 48.9 | 51.1 | 53.3 | 62.2 | 80.0 |
15 | 33 | 30.3 | 36.4 | 36.4 | 36.4 | 36.4 | 36.4 | 42.4 | 57.6 |
16 | 29 | 27.6 | 34.5 | 34.5 | 41.4 | 44.8 | 44.8 | 48.3 | 51.7 |
17 | 12 | 41.7 | 41.7 | 41.7 | 50.0 | 50.0 | 50.0 | 58.3 | 58.3 |
18 | 25 | 36.0 | 40.0 | 40.0 | 44.0 | 44.0 | 44.0 | 48.0 | 52.0 |
19 | 21 | 57.1 | 61.9 | 61.9 | 61.9 | 66.7 | 66.7 | 66.7 | 71.4 |
20 | 16 | 43.8 | 50.0 | 50.0 | 50.0 | 50.0 | 50.0 | 50.0 | 50.0 |
21 | 21 | 33.3 | 42.9 | 42.9 | 42.9 | 42.9 | 47.6 | 57.1 | 57.1 |
22 | 21 | 57.1 | 61.9 | 61.9 | 61.9 | 61.9 | 61.9 | 61.9 | 71.4 |
23 | 10 | 50.0 | 50.0 | 50.0 | 50.0 | 50.0 | 50.0 | 50.0 | 50.0 |
24 | 17 | 41.2 | 41.2 | 47.1 | 47.1 | 47.1 | 47.1 | 47.1 | 52.9 |
25 | 15 | 60.0 | 60.0 | 60.0 | 60.0 | 60.0 | 60.0 | 66.7 | 66.7 |
26 | 10 | 40.0 | 40.0 | 40.0 | 40.0 | 40.0 | 40.0 | 40.0 | 40.0 |
27 | 10 | 20.0 | 30.0 | 30.0 | 30.0 | 30.0 | 30.0 | 30.0 | 30.0 |
28 | 14 | 35.7 | 42.9 | 42.9 | 42.9 | 50.0 | 50.0 | 50.0 | 57.1 |
29 | 14 | 21.4 | 21.4 | 21.4 | 21.4 | 21.4 | 21.4 | 21.4 | 28.6 |
30 | 5 | 60.0 | 60.0 | 60.0 | 60.0 | 60.0 | 60.0 | 60.0 | 60.0 |
All | 910 | 61.6 | 68.7 | 71.5 | 74.3 | 75.4 | 76.0 | 79.0 | 82.9 |