Table 1 Validation of MDPA method using the CCDC/Astex dataset
From: A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions
Entry | Prediction | Ligand-binding Site | Ligand orientation | ||||
|---|---|---|---|---|---|---|---|
PDB | Chain | Cluster | MCC | Precision | Recall | Precision | Recall |
1g9v | A | O | 0.45 | 0.32 | 0.86 | 0.76 | 0.98 |
1gkc | A | O | 0.56 | 0.47 | 0.75 | 0.76 | 0.73 |
1gm8 | B | R | 0.63 | 1.00 | 0.40 | 1.00 | 0.71 |
1gpk | A | O | 0.41 | 0.23 | 0.83 | 0.32 | 0.94 |
1hnn | A | O | 0.48 | 0.34 | 0.84 | 0.49 | 1.00 |
1hp0 | A | O | 0.69 | 0.50 | 1.00 | 0.93 | 1.00 |
1hq2 | A | O | 0.51 | 0.34 | 0.92 | 0.69 | 1.00 |
1hvy | A | O | 0.38 | 0.21 | 0.82 | 0.41 | 0.81 |
1hwi | AB | O | 0.26 | 0.25 | 0.29 | 0.00 | 0.00 |
1hww | A | P | 0.15 | 0.25 | 0.09 | 0.00 | 0.00 |
1ia1 | A | O | 0.49 | 0.35 | 0.80 | 0.58 | 1.00 |
1ig3† | B | O | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
1j3j | A | O | 0.55 | 0.42 | 0.80 | 0.88 | 1.00 |
1jd0 | A | O | 0.47 | 0.32 | 0.78 | 0.49 | 1.00 |
1jje | A | O | 0.49 | 0.33 | 0.82 | 0.61 | 1.00 |
1jla | A | O | 0.22 | 0.13 | 0.44 | 0.14 | 0.33 |
1k3u | A | O | 0.52 | 0.33 | 0.93 | 0.48 | 1.00 |
1ke5 | A | O | 0.14 | 0.18 | 0.17 | 0.78 | 0.13 |
1kzk | A | O | 0.49 | 0.55 | 0.55 | 0.45 | 0.44 |
1l2s | A | O | 0.41 | 0.21 | 0.88 | 0.38 | 1.00 |
1l7f | A | O | 0.37 | 0.29 | 0.54 | 0.54 | 1.00 |
1lpz | B | O | 0.60 | 0.62 | 0.62 | 0.87 | 0.88 |
1lrh | A | O | 0.52 | 0.35 | 0.89 | 0.79 | 1.00 |
1m2z | A | O | 0.17 | 0.22 | 0.18 | 0.00 | 0.00 |
1meh | A | O | 0.46 | 0.60 | 0.38 | 0.67 | 0.30 |
1mmv | A | O | 0.11 | 0.09 | 0.22 | 0.46 | 0.74 |
1mzc | B | O | 0.07 | 0.08 | 0.10 | 0.00 | 0.00 |
1n1m* | A | O | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
1n2j | A | O | 0.29 | 0.12 | 0.83 | 0.26 | 1.00 |
1n2v | A | O | 0.50 | 0.30 | 0.89 | 0.62 | 1.00 |
1n46 | A | O | 0.01 | 0.08 | 0.06 | 0.00 | 0.00 |
1nav | A | O | 0.48 | 0.45 | 0.60 | 1.00 | 0.87 |
1of1 | A | O | 0.82 | 0.78 | 0.88 | 1.00 | 1.00 |
1of6 | A | O | 0.66 | 0.71 | 0.62 | 0.40 | 0.62 |
1opk | A | O | 0.07 | 0.05 | 0.17 | 0.00 | 0.00 |
1oq5 | A | O | 0.60 | 0.39 | 1.00 | 0.67 | 1.00 |
1owe | A | O | 0.50 | 0.27 | 1.00 | 0.29 | 1.00 |
1oyt | H | O | 0.51 | 0.43 | 0.69 | 0.73 | 0.97 |
1p2y* | A | O | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
1p62 | B | O | 0.48 | 0.36 | 0.73 | 0.88 | 1.00 |
1pmm | A | O | 0.38 | 0.38 | 0.42 | 0.55 | 0.60 |
1q1g | A | O | 0.44 | 0.31 | 0.73 | 0.58 | 1.00 |
1q41 | A | O | 0.06 | 0.07 | 0.12 | 0.50 | 0.29 |
1q4g | A | O | 0.45 | 0.24 | 0.88 | 0.31 | 1.00 |
1r1h* | A | O | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
1r55 | A | O | 0.65 | 0.59 | 0.77 | 0.83 | 0.83 |
1r58 | A | O | 0.52 | 0.41 | 0.70 | 0.83 | 0.70 |
1r9o | A | O | 0.26 | 0.13 | 0.62 | 0.10 | 0.39 |
1s19 | A | O | 0.52 | 0.33 | 0.92 | 0.98 | 0.97 |
1s3v | A | O | 0.57 | 0.53 | 0.69 | 0.89 | 0.48 |
1sg0 | AB | O | 0.45 | 0.29 | 0.75 | 0.50 | 0.10 |
1sj0 | A | O | 0.49 | 0.50 | 0.54 | 0.82 | 0.33 |
1sq5 | A | O | 0.54 | 0.58 | 0.54 | 0.29 | 0.48 |
1sqn | A | O | 0.21 | 0.17 | 0.38 | 0.00 | 0.00 |
1t40 | A | O | 0.48 | 0.42 | 0.62 | 0.59 | 0.96 |
1t46 | A | O | 0.39 | 0.36 | 0.50 | 0.34 | 0.51 |
1t9b | A | O | 0.40 | 0.33 | 0.50 | 0.85 | 0.52 |
1tow | A | O | 0.16 | 0.10 | 0.67 | 0.50 | 0.95 |
1tt1 | A | O | 0.69 | 0.78 | 0.64 | 1.00 | 0.73 |
1tz8 | AB | O | 0.72 | 0.23 | 0.57 | 0.22 | 0.50 |
1u1c | A | O | 0.38 | 0.23 | 0.78 | 0.54 | 1.00 |
1u4d | A | O | 0.47 | 0.28 | 0.89 | 0.47 | 0.94 |
1uml | A | O | 0.63 | 0.41 | 1.00 | 0.74 | 1.00 |
1unl | A | O | 0.28 | 0.28 | 0.36 | 0.87 | 0.54 |
1uou* | A | O | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
1v0p | A | O | 0.53 | 0.71 | 0.42 | 1.00 | 0.33 |
1v48 | A | P | 0.65 | 0.69 | 0.64 | 0.77 | 0.91 |
1v4s | A | O | 0.73 | 0.71 | 0.77 | 1.00 | 0.61 |
1vcj | A | O | 0.35 | 0.33 | 0.42 | 0.85 | 1.00 |
1w1p | A | O | 0.27 | 0.07 | 1.00 | 0.17 | 1.00 |
1w2g | A | O | 0.29 | 0.11 | 1.00 | 0.07 | 1.00 |
1 × 8x | A | P | 0.20 | 0.17 | 0.33 | 0.37 | 0.69 |
1xm6 | A | O | 0.47 | 0.31 | 0.8 | 0.58 | 1.00 |
1xoq | A | O | 0.59 | 0.43 | 0.87 | 0.56 | 1.00 |
1xoz | A | O | 0.36 | 0.25 | 0.6 | 0.39 | 0.66 |
1y6b | A | O | 0.56 | 0.48 | 0.71 | 0.81 | 0.79 |
1ygc | H | O | 0.47 | 0.50 | 0.50 | 0.96 | 0.89 |
1yqy | A | Q | 0.3 | 0.43 | 0.23 | 0.44 | 0.43 |
1yv3 | A | P | 0.38 | 0.50 | 0.31 | 0.35 | 0.48 |
1yvf | A | P | 0.31 | 0.10 | 1.00 | 0.16 | 1.00 |
1ywr | A | O | 0.53 | 0.40 | 0.77 | 0.70 | 0.97 |
1z95 | A | O | 0.22 | 0.23 | 0.33 | 0.00 | 0.00 |
2bm2 | A | P | 0.48 | 0.56 | 0.45 | 0.25 | 0.03 |
2br1 | A | O | 0.39 | 0.30 | 0.58 | 0.40 | 0.45 |
2bsm | A | O | 0.52 | 0.43 | 0.71 | 0.78 | 0.78 |