Table 1.
Performance of FV structure prediction methods on benchmarks
| Method | OCD | H Fr (Å) | H1 (Å) | H2 (Å) | H3 (Å) | L Fr (Å) | L1 (Å) | L2 (Å) | L3 (Å) |
|---|---|---|---|---|---|---|---|---|---|
| RosettaAntibody benchmark | |||||||||
| RosettaAntibody-G | 5.19 | 0.57 | 1.22 | 1.14 | 3.48 | 0.67 | 0.80 | 0.87 | 1.06 |
| RepertoireBuilder | 5.26 | 0.58 | 0.86 | 1.00 | 2.94 | 0.51 | 0.63 | 0.52 | 1.03 |
| ABodyBuilder | 4.69 | 0.50 | 0.99 | 0.88 | 2.94 | 0.49 | 0.72 | 0.52 | 1.09 |
| DeepAb | 3.67 | 0.43 | 0.72 | 0.85 | 2.33 | 0.42 | 0.55 | 0.45 | 0.86 |
| Therapeutic benchmark | |||||||||
| RosettaAntibody-G | 5.43 | 0.63 | 1.42 | 1.05 | 3.77 | 0.55 | 0.89 | 0.83 | 1.48 |
| RepertoireBuilder | 4.37 | 0.62 | 0.91 | 0.96 | 3.13 | 0.47 | 0.71 | 0.52 | 1.08 |
| ABodyBuilder | 4.37 | 0.49 | 1.05 | 1.02 | 3.00 | 0.45 | 1.04 | 0.50 | 1.35 |
| DeepAb | 3.52 | 0.40 | 0.77 | 0.68 | 2.52 | 0.37 | 0.60 | 0.42 | 1.02 |
Orientational coordinate distance (OCD) is a unitless quantity calculated by measuring the deviation from native of four heavy-light chain coordinates.8 Heavy chain framework (H Fr) and light chain framework (L Fr) RMSDs are measured after superimposing the heavy and light chains, respectively. CDR loop RMSDs are measured using the Chothia loop definitions after superimposing the framework region of the corresponding chain. All RMSDs are measured over backbone heavy atoms.