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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 (Å) 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