Table 1. Summary of free energy calculation results based on crystal structures. ΔGcalc is the calculated standard binding free energy; ΔGexp is the experimental standard binding free energy. Reported are also the PDB files used as input and the experimental method used for the affinity measurement. All values are in kcal mol–1 α. All errors are one standard deviation. This is an estimate of the typical ITC standard deviation (1σ) based on the variability of the affinity values observed in the ABRF-MIRG′02 inter-laboratory assessment;67βthe error represents the standard deviation of two measurements; γno error reported as only a single experiment was performed. Values for the difference between ΔGcalc and ΔGexp might appear inconsistent due to rounding.
Cpd | ΔGcalc | ΔGexp | ΔGcalc–ΔGexp | PDB | Exp method | Reference |
1 | –10.4 ± 0.6 | –9.8 ± 0.1α | –0.6 ± 0.6 | 4OGI | ITC | 68 |
2 | –9.5 ± 0.4 | –9.6 ± 0.1α | +0.2 ± 0.4 | 3MXF | ITC | 69 |
3 | –9.2 ± 0.5 | –9.0 ± 0.1α | –0.2 ± 0.5 | 4MR3 | ITC | 70 |
4 | –9.4 ± 0.8 | –8.9 ± 0.1α | –0.4 ± 0.8 | 4OGJ | ITC | 68 |
5 | –8.6 ± 0.3 | –8.8 ± 0.1β | +0.2 ± 0.3 | 4J0R | SPR | 71 |
6 | –9.9 ± 0.8 | –8.2 ± 0.1α | –1.7 ± 0.8 | 3U5L | ITC | 72 |
7 | –5.9 ± 0.5 | –7.8 ± 0.1α | +2.0 ± 0.5 | 4MR4 | ITC | 70 |
8 | –7.8 ± 0.3 | –7.4 ± 0.1α | –0.4 ± 0.3 | 3U5J | ITC | 72 |
9 | –7.7 ± 0.4 | –7.3 ± 0.0β | –0.4 ± 0.4 | 3SVG | AlphaScreen | 71 |
10 | –5.9 ± 0.2 | –6.3 ± 0.1β | +0.4 ± 0.3 | 4HBV | AlphaScreen | 73 |
11 | –5.4 ± 0.2 | –5.6γ | +0.1 ± 0.2 | Model | AlphaScreen | 74 |
Statistics | |
Mean absolute error | 0.6 ± 0.1 |
Root mean square error | 0.8 ± 0.2 |
Pearson's r | 0.84 ± 0.05 |
Spearman's ρ | 0.82 ± 0.06 |