Table 2. Quality assessments of M1AP models from five different algorithms.
Initial and comparison models were not assessed after being processed with molecular dynamics (MD) simulations whereas further and variant models were assessed after being subjected to MD simulations for a time period specified at the end of the model name (e.g., 450ns).
| Model | VERIFY3D2 | ERRAT3 | PROVE4 | PROCHECK5 | WHATCHECK6 | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Aa1% with score ≥0.2 | AOQF1% | BOPA1% | Aa% in MFR1 | Aa% in AAR1 | Aa% in GAR1 | Aa% in DR1 | G-Factor | # of SCP1 with pass | # of SCP with warning | # of SCP with error | Overall report | |
| Initial Models | ||||||||||||
| GalaxyWeb | 69.25 | 74.07 | 8.1 | 89.1 | 8.4 | 1.7 | 0.8 | –0.05 | 26 | 15 | 4 | Pass |
| I-TASSER | 47.36 | 90.47 | 7.5 | 60.8 | 31.7 | 4.7 | 2.8 | –0.77 | 19 | 18 | 10 | Pass |
| Phyre2 | 56.98 | 22.99 | 10.4 | 76.0 | 14.6 | 5.1 | 4.3 | –0.60 | 27 | 12 | 7 | Pass |
| PRIMO | 39.66 | 1.35 | 33.4 | 58.4 | 25.1 | 9.2 | 7.3 | –1.41 | 23 | 15 | 8 | Pass |
| RaptorX | 41.32 | 43.72 | 9.1 | 78.6 | 17.8 | 1.9 | 1.7 | –0.42 | 23 | 16 | 7 | Pass |
| Robetta | 76.23 | 95.22 | 4.8 | 83.9 | 15.6 | 0.3 | 0.2 | 0.11 | 27 | 14 | 6 | Pass |
| Robetta-domain | 89.06 | 88.24 | 4.4 | 85.2 | 13.9 | 0.5 | 0.4 | 0.20 | 27 | 15 | 5 | Pass |
| Comparison Model | ||||||||||||
| AlphaFold2 | 89.55 | 63.21 | 4.4 | 80.9 | 14.3 | 3.5 | 1.3 | –0.14 | 22 | 17 | 6 | Pass |
| Further Models | ||||||||||||
| GalaxyWeb_100ns | 88.30 | 78.35 | 7.1 | 84.6 | 13.7 | 1.1 | 0.6 | –1.11 | 17 | 21 | 8 | Pass |
| Robetta-domain_100ns | 83.89 | 87.53 | 6.6 | 87.1 | 10.7 | 1.3 | 0.9 | –1.11 | 17 | 21 | 8 | Pass |
| GalaxyWeb_450ns | 80.75 | 85.38 | 5.9 | 89.1 | 9.4 | 1.3 | 0.2 | –1.05 | 17 | 22 | 7 | Pass |
| Variant Models | ||||||||||||
| GalaxyWeb_Ser50Pro_450ns | 79.62 | 87.45 | 8.5 | 88.0 | 9.2 | 2.4 | 0.4 | –1.10 | 16 | 22 | 8 | Pass |
| GalaxyWeb_Arg266Gln_450ns | 86.60 | 77.26 | 6.0 | 84.6 | 12.6 | 1.9 | 0.9 | –1.14 | 16 | 20 | 10 | Pass |
| GalaxyWeb_Gly317Arg_450ns | 84.91 | 74.90 | 7.1 | 85.5 | 12.4 | 1.1 | 1.0 | –1.09 | 18 | 20 | 8 | Pass |
| GalaxyWeb_Pro389Leu_450ns | 77.36 | 70.50 | 8.2 | 84.2 | 13.0 | 1.7 | 1.1 | –1.11 | 16 | 21 | 9 | Pass |
| GalaxyWeb_Leu430Pro_450ns | 79.06 | 78.46 | 6.3 | 85.6 | 12.0 | 1.7 | 0.7 | –1.09 | 18 | 20 | 8 | Pass |
Notes:
Aa, amino acid; AOQF, average overall quality factor; BOPA, buried outlier protein atoms; MFR, the most favored regions; AAR, additional allowed regions; GAR, generously allowed regions; DR, disallowed regions; SCP, stereochemical properties.
In VERIFY3D, at least 80% of aa in a protein should have a score ≥0.2 in the 3D–1D profile for a good quality.
In ERRAT, AOQF ≥95% indicates a good quality, AOQF around 91% indicates an average quality, and lower AOQF indicates a bad quality.
In PROVE, BOPA ≤1% indicates a good quality, BOPA between 1% and 5% indicates an average quality, and BOPA >5% indicates a bad quality.
In the Ramachandran plot analysis of PROCHECK, model has a good quality if overall G-factor is >–0.5 and ≥90% of aa in protein are in the most favored regions.
In WHATCHECK, SCP with pass refers to a good quality, SCP with warning indicates an average quality, and SCP with error refers to a bad quality. Of note, total number of SCP might vary from structure to structure.