Table 2.
Comparison between NMA and WSAS in TS (T = 298.15 K) calculations for 22 proteins and 2 nucleic acids.
| PDB_ID | Data Type | TS by NMA * | TS by WSAS * | Linear Regression ** | ||
|---|---|---|---|---|---|---|
| R2 | AUE | RMSE | ||||
| Protein-Ligand Complexes | ||||||
| 1A9U | Complex | 3949.05±10.88 | 3990.36±4.29 | 0.83 | 6.41 | 7.24 |
| Ligand | 47.97±0.00 | 46.80±0.02 | 0.00 | 0.01 | 0.02 | |
| Protein | 3922.79±11.72 | 3963.93±4.57 | 0.76 | 7.43 | 8.10 | |
| Binding | 21.71±4.00 | 20.37±1.83 | 0.61 | 2.05 | 2.76 | |
| 1A9U truncated R = 8 Å | Complex | 337.24±2.07 | 281.04±0.92 | 0.61 | 1.20 | 1.40 |
| Ligand | 47.97±0.00 | 46.80±0.01 | 0.00 | 0.01 | 0.01 | |
| Protein | 304.44±2.86 | 248.29±1.39 | 0.54 | 1.94 | 1.98 | |
| Binding | 15.16±3.72 | 14.05±1.40 | 0.55 | 2.52 | 2.79 | |
| 1A9U truncated R = 10 Å | Complex | 497.22±2.16 | 435.34±1.69 | 0.80 | 0.81 | 0.97 |
| Ligand | 47.97±0.00 | 46.80±0.01 | 0.00 | 0.01 | 0.01 | |
| Protein | 465.78±3.03 | 406.17±1.97 | 0.82 | 1.11 | 1.39 | |
| Binding | 16.53±3.07 | 17.63±2.56 | 0.72 | 1.35 | 1.65 | |
| 1A9U truncated R = 12 Å | Complex | 698.80±1.96 | 639.32±1.11 | 0.32 | 1.26 | 1.62 |
| Ligand | 47.97±0.00 | 46.80±0.01 | 0.00 | 0.01 | 0.01 | |
| Protein | 672.33±2.87 | 612.42±1.71 | 0.38 | 1.80 | 2.25 | |
| Binding | 21.49±3.02 | 19.90±2.12 | 0.76 | 1.14 | 1.52 | |
| 1A9U truncated R = 15 Å | Complex | 1125.27±6.65 | 1042.01±2.47 | 0.70 | 3.72 | 4.65 |
| Ligand | 47.97±0.00 | 46.80±0.01 | 0.00 | 0.01 | 0.01 | |
| Protein | 1098.35±3.04 | 1016.40±1.98 | 0.45 | 1.77 | 2.25 | |
| Binding | 21.05±6.89 | 21.19±2.85 | 0.80 | 3.39 | 4.51 | |
| 1ABE | Complex | 3249.00±4.45 | 3278.36±3.18 | 0.63 | 2.04 | 2.74 |
| Ligand | 29.24±0.04 | 28.33±0.02 | 0.78 | 0.02 | 0.03 | |
| Protein | 3232.34±5.41 | 3265.31±2.56 | 0.53 | 2.94 | 3.98 | |
| Binding | 12.59±2.53 | 15.29±1.70 | 0.50 | 1.34 | 1.84 | |
| 1AHA | Complex | 2715.46±5.04 | 2726.63±3.12 | 0.42 | 3.32 | 3.82 |
| Ligand | 25.22±0.00 | 23.51±0.01 | 0.00 | 0.01 | 0.01 | |
| Protein | 2704.94±4.31 | 2715.87±3.26 | 0.37 | 2.99 | 3.48 | |
| Binding | 14.71±3.44 | 12.75±2.17 | 0.80 | 1.44 | 1.65 | |
| 1FKG | Complex | 1232.21±3.38 | 1233.20±1.46 | 0.00 | 3.01 | 3.60 |
| Ligand | 61.60±0.00 | 60.93±0.01 | 0.00 | 0.01 | 0.01 | |
| Protein | 1193.46±3.66 | 1193.86±1.46 | 0.05 | 2.56 | 3.62 | |
| Binding | 22.85±2.45 | 21.59±1.37 | 0.40 | 1.48 | 1.90 | |
| 1FKI | Complex | 2427.95±4.40 | 2440.44±1.87 | 0.07 | 3.63 | 4.28 |
| Ligand | 59.59±0.16 | 62.97±0.13 | 0.99 | 0.03 | 0.04 | |
| Protein | 2384.62±5.92 | 2395.56±1.71 | 0.62 | 4.03 | 4.70 | |
| Binding | 16.26±3.59 | 18.09±2.16 | 0.71 | 1.79 | 2.22 | |
| 1HPV | Complex | 2218.89±5.06 | 2218.38±2.84 | 0.42 | 2.90 | 3.88 |
| Ligand | 67.71±0.02 | 64.29±0.03 | 0.40 | 0.04 | 0.05 | |
| Protein | 2181.30±6.46 | 2182.79±2.71 | 0.37 | 3.93 | 5.27 | |
| Binding | 30.11±4.83 | 28.71±1.03 | 0.67 | 3.38 | 4.00 | |
| 1HPV truncated R = 8 Å | Complex | 406.48±2.66 | 340.28±0.98 | 0.53 | 1.59 | 1.97 |
| Ligand | 67.71±0.02 | 64.29±0.03 | 0.40 | 0.04 | 0.05 | |
| Protein | 359.91±2.91 | 294.81±2.02 | 0.59 | 1.58 | 1.87 | |
| Binding | 21.14±3.46 | 18.82±2.00 | 0.16 | 2.95 | 3.30 | |
| 1HPV truncated R =10 Å | Complex | 582.00±2.88 | 523.89±0.95 | 0.01 | 2.56 | 2.98 |
| Ligand | 67.71±0.02 | 64.29±0.03 | 0.40 | 0.04 | 0.05 | |
| Protein | 540.15±3.14 | 482.95±2.62 | 0.69 | 1.18 | 1.78 | |
| Binding | 25.86±4.99 | 23.35±2.43 | 0.62 | 2.66 | 3.30 | |
| 1HPV truncated R = 12 Å | Complex | 770.23±1.62 | 712.70±0.84 | 0.34 | 1.09 | 1.32 |
| Ligand | 67.71±0.02 | 64.29±0.03 | 0.40 | 0.04 | 0.05 | |
| Protein | 727.74±3.44 | 670.24±1.86 | 0.88 | 1.47 | 1.70 | |
| Binding | 25.22±3.73 | 21.83±1.96 | 0.71 | 1.74 | 2.18 | |
| 1HPV truncated R = 15 ) | Complex | 1135.37±3.60 | 1081.09±1.57 | 0.68 | 1.89 | 2.43 |
| Ligand | 67.71±0.02 | 64.29±0.03 | 0.40 | 0.04 | 0.05 | |
| Protein | 1093.99±6.84 | 1041.29±2.58 | 0.73 | 3.97 | 4.75 | |
| Binding | 26.33±5.54 | 24.49±2.36 | 0.59 | 3.53 | 3.94 | |
| 3PTB | Complex | 2296.37±6.80 | 2302.52±3.27 | 0.74 | 3.60 | 4.32 |
| Ligand | 25.81±0.00 | 24.73±0.01 | 0.00 | 0.08 | 0.00 | |
| Protein | 2286.18±7.17 | 2294.37±3.35 | 0.78 | 3.37 | 4.51 | |
| Binding | 15.63±3.35 | 16.58±0.93 | 0.87 | 2.05 | 2.55 | |
| 4PHV | Complex | 2246.00±5.68 | 2237.64±2.13 | 0.77 | 3.27 | 3.95 |
| Ligand | 78.26±0.38 | 73.52±0.09 | 0.80 | 0.28 | 0.30 | |
| Protein | 2195.60±7.73 | 2192.79±3.34 | 0.85 | 3.98 | 4.83 | |
| Binding | 27.85±8.64 | 28.67±2.76 | 0.86 | 5.65 | 6.21 | |
| Protein-Peptide Complexes | ||||||
| 1BE9 | Complex | 1306.77±4.98 | 1315.13±2.34 | 0.25 | 3.72 | 4.31 |
| Peptide | 84.32±0.29 | 79.40±0.12 | 0.71 | 0.16 | 0.20 | |
| Protein | 1255.68±4.74 | 1259.23±1.35 | 0.07 | 3.60 | 4.58 | |
| Binding | 33.23±6.03 | 23.51±2.33 | 0.82 | 2.81 | 3.33 | |
| 1HEF | Complex | 1179.50±5.45 | 1178.84±2.67 | 0.59 | 3.25 | 3.79 |
| Peptide | 90.76±0.57 | 86.93±0.18 | 0.07 | 0.46 | 0.55 | |
| Protein | 1115.50±4.54 | 1114.67±2.58 | 0.89 | 1.97 | 2.27 | |
| Binding | 26.76±6.74 | 22.76±2.89 | 0.83 | 3.05 | 3.87 | |
| 8GCH | Complex | 2491.53±4.47 | 2489.09±3.05 | 0.33 | 2.99 | 3.68 |
| Peptide | 50.23±0.90 | 46.70±0.30 | 0.82 | 0.50 | 0.62 | |
| Protein | 2467.12±3.30 | 2463.14±3.32 | 0.69 | 1.54 | 1.93 | |
| Binding | 25.82±5.62 | 20.75±2.93 | 0.85 | 1.89 | 2.67 | |
| Protein Receptors | ||||||
| 1FL0 | Protein | 1817.62±6.65 | 1823.04±2.52 | 0.47 | 4.19 | 5.25 |
| 1KOE | Protein | 1859.37±7.42 | 1859.16±2.78 | 0.85 | 4.16 | 4.97 |
| 1LMI | Protein | 1380.58±3.97 | 1381.46±2.38 | 0.89 | 1.63 | 1.89 |
| Nucleic Acids | ||||||
| 195D | Complex | 645.24±2.28 | 658.07±1.45 | 0.80 | 0.98 | 1.19 |
| Ligand | 65.72±0.50 | 57.99±0.08 | 0.63 | 0.38 | 0.43 | |
| DNA | 611.69±3.06 | 625.47±1.81 | 0.42 | 2.17 | 2.34 | |
| Binding | 32.18±3.64 | 25.39±2.10 | 0.50 | 2.01 | 2.57 | |
| 422D | RNA | 668.23±5.02 | 658.56±2.55 | 0.88 | 2.32 | 2.75 |
*
For each TS by NMA or WSAS, the mean and the RMS deviation were estimated using 10 data points calculated using 10 MD snapshots.
**
The performance of a linear regression is measured by correlation coefficient square, the average unsigned error (AUE) and root-mean-square error (RMSE).