Table 3.
ΔGDT-HA, ΔRMSD, MolProbity and ΔSphereGrinder values after refinement from sampling in the presence of lipid bilayers with different membrane widths.
| 1j4n | 1qj8 | 3vg9 | 4hyj | 4kr8 | Ave. | Ave. DPPC | |
|---|---|---|---|---|---|---|---|
| ΔGDT-HA | |||||||
| RWplus | −1.90 | 12.67 | −2.35 | 3.28 | −2.94 | 1.75±2.95 | 2.28±2.46 |
| DFIRE | −1.80 | 13.01 | −2.44 | 3.60 | −2.35 | 2.00±2.97 | 2.09±2.35 |
| HDGBv3 | −2.10 | 12.33 | −1.34 | 3.50 | −2.35 | 2.01±2.79 | 2.10±2.36 |
| HDGBvdW | −2.51 | 12.33 | −1.85 | 3.60 | −1.69 | 1.98±2.81 | 1.92±2.36 |
| ΔRMSD [Å] | |||||||
| RWplus | −0.08 | −0.47 | −0.07 | −0.15 | −0.04 | −0.16±0.08 | −0.15±0.08 |
| DFIRE | −0.08 | −0.49 | −0.07 | −0.14 | −0.05 | −0.17±0.08 | −0.14±0.08 |
| HDGBv3 | −0.09 | −0.47 | −0.08 | −0.14 | −0.04 | −0.16±0.08 | −0.14±0.08 |
| HDGBvdW | −0.08 | −0.47 | −0.07 | −0.14 | −0.04 | −0.16±0.08 | −0.14±0.08 |
| MolProbity | |||||||
| RWplus | 0.95 | 0.53 | 0.99 | 0.87 | 0.68 | 0.80±0.09 | 0.84±0.07 |
| DFIRE | 0.91 | 0.65 | 1.02 | 0.87 | 0.71 | 0.83±0.07 | 0.82±0.06 |
| HDGBv3 | 0.95 | 0.53 | 0.90 | 0.84 | 0.71 | 0.79±0.08 | 0.84±0.05 |
| HDGBvdW | 0.95 | 0.53 | 1.02 | 0.87 | 0.71 | 0.82±0.09 | 0.81±0.05 |
| ΔSphereGrinder | |||||||
| RWplus | −0.21 | 9.03 | 0.18 | 1.8 | 3.92 | 2.94±1.67 | 3.49±2.29 |
| DFIRE | −0.21 | 9.72 | 0.18 | −0.23 | 0.9 | 2.07±1.92 | 2.40±2.55 |
| HDGBv3 | 0.0 | 8.33 | 0.89 | −0.23 | 0.45 | 1.89±1.62 | 2.51±2.19 |
| HDGBvdW | −0.43 | 9.03 | 1.07 | −0.23 | 0.6 | 2.01±1.78 | 2.58±2.43 |
Lipid types were selected according to the hydrophobic length of the homology model (see ‘Lipid Type’ in Table 1). Average values over the five proteins with varying lipid types are compared (column labeled by Ave.) with averages for DPPC simulations (Ave. DPPC) for the same set of proteins (1j4n, 1qj8, 3vg9, 4hyj and 4kr8).