Table 2. Summary of ZIKV homology models and statistical validation.
The global and per-residue model quality has been assessed using the QMEAN scoring function 53. For improved performance, weights of the individual QMEAN terms have been trained specifically for SWISS-MODEL 50, 51, 71– 73. GMQE = Global Model Quality Estimation, QMEAN4 is a scoring function consisting of a linear combination of four structural descriptors as described elsewhere in more detail 52, 53.
| Zika Protein | Template | Coverage | Sequence
Identity |
GMQE | MEAN4 | PROCHECK analysis | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Organism | Protein | PDB
code |
Most
favored regions |
Additional
allowed regions |
Generously
allowed regions |
Disallowed
regions |
|||||
| NS5 | Japanese
encephalitis virus |
NS5 61 | 4K6M | 100% | 53% | 0.89 | -2.80 | 66.3% | 30.9% | 2.3% | 0.9% |
| FtsJ | West Nile
virus |
methyltransferase 62 | 2OY0 | 99% | 54% | 0.94 | -1.23 | 69.5% | 27.7% | 2.1% | 0.7% |
| HELICc | Dengue virus | helicase/nucleoside
triphosphatase catalytic domain 63 |
2BHR | 100% | 55% | 0.94 | -1.60 | 69.3% | 27.7% | 2.0% | 1.0% |
| DEXDc | Murray Valley
encephalitis virus |
RNA helicase 64 | 2V8O | 100% | 54% | 0.93 | -0.92 | 70.3% | 27.3% | 1.6% | 0.8% |
| Peptidase S7 | West Nile
virus |
Ns2B-Ns3 protease 65 | 2YOL | 100% | 53% | 0.92 | -0.25 | 67.5% | 28.3% | 4.2% | 0.0% |
| NS1 | West Nile
virus |
non-structural protein 1 66 | 4O6D | 99% | 48% | 0.77 | -4.09 | 58.4% | 36.3% | 3.3% | 2.0% |
| E Stem | Dengue virus | capsid protein 67 | 3J2P | 100% | 46% | 0.74 | -8.02 | 62.5% | 27.5% | 6.3% | 3.8% |
| Glycoprotein M | Dengue virus | cryo-EM structure of
virus 67 |
3J27 | 100% | 40% | 0.73 | -6.90 | 60.6% | 28.8% | 4.5% | 6.1% |
| Propeptide | Dengue virus | precursor membrane
protein-envelope 68 |
3C5X | 87% | 47% | 0.74 | -0.70 | 53.7% | 43.3% | 1.5% | 1.5% |
| Capsid | West Nile
virus |
core (C) protein 69 | 1SFK | 65% | 42% | 0.50 | -3.54 | 69.5% | 27.1% | 3.4% | 0.0% |
| Glycoprotein E | Japanese
encephalitis virus |
envelope glycoprotein 70 | 3P54 | 99% | 47% | 0.81 | -3.76 | 63.5% | 31.3% | 3.7% | 1.4% |
| NS4A | ─ | ─ | 20% | 29% | 0.07 | -1.75 | ─ | ─ | ─ | ─ | |
| NS2B | ─ | ─ | 37% | 48% | 0.21 | -0.49 | ─ | ─ | ─ | ─ | |
| NS2A | ─ | ─ | 16% | 31% | 0.04 | -3.10 | ─ | ─ | ─ | ─ | |
| NS4B | ─ | ─ | 14% | 30% | 0.03 | -2.81 | ─ | ─ | ─ | ─ | |