Table 6.
Quality check for models generated using ABodyBuilder (ABB), ABlooper (ABL), IgFold (IgF), EquiFold (EqF), AlphaFold-Multimer (AFM) and ABodyBuilder2 (AB2).
| Method | Peptide bond | D-amino acid | Cis-bond | Clash |
|---|---|---|---|---|
| Xtal | 0 | 0 | 0 | 0 |
| ABB | 19 | 0 | 3 | 9 |
| ABL* | 1 | 0 | 1 | 1 |
| IgF | 0 | 0 | 51 | 10 |
| EqF | 271 | 4 | 2 | 765 |
| AFM | 0 | 0 | 0 | 0 |
| AB2 | 0 | 0 | 0 | 0 |
The errors observed in experimentally resolved crystal structures (Xtal) are also shown for comparison. A peptide bond length is considered to be incorrect if it is more than 0.1 Å away from its literature value. Peptide bonds including a proline were not included in the calculation of cis-isomers. Two non-bonded heavy atoms are considered to be clashing when they are closer than 0.63 times their Van-der-Waals radius39. (*) Calculated using the latest version of ABlooper, updated since publication to reduce the number of D-amino acids and cis-isomers.