(a) Schematic for CDR heavy chain loops. (b) The CDR lengths of monoclonal antibodies (mAbs) (n = 47) and nanobodies (Nbs) (n = 78). The error bars represent the standard deviation of the data. (c) …
(a) The performance of AlphaFold2 in DB1 relative to other methods after superimposing Fv backbones. (b) The performance of H3-OPT in DB1 relative to other methods after superimposing VH backbones. …
(a) Side-by-side comparison of backbone and CDR3 heavy atom root mean square deviations (RMSDs) for DeepAb and AlphaFold2 in DB1. (b) Side-by-side comparison of backbone and CDR3 heavy atom RMSDs …
(a) Comparison of CDR-H3 loops of MD (gray), AF2 (pink), and experimentally determined structure (cyan). (b) Root mean square fluctuation (RMSF) of antibody residues during simulation. CDR-H3 loop …
(a) Schematic for dataset preparation. Structures were screened from the SAbDab database based on resolution and sequence identity. Clustering of the filtered, high-resolution structures yielded …
(a) Side-by-side comparison of Cα-RMSDs of AF2 and IgFold for Sub1 (n = 52); color scale for data points reflects CDR3 length. AF2 outperformed IgFold for targets left of the dashed diagonal; IgFold …
(a) Side-by-side comparison of Cα-RMSDs for AF2 and IgFold, IgFold and H3-OPT in the Sub2 (n = 46) and Sub3 (n = 33) test sets, respectively. (b) Comparison of prediction accuracy between AF2 and …
(a) The performance of H3-OPT in the test set (nmAbs = 119, nNbs = 12) relative to other methods. The RMSDCα of H3-OPT was significantly lower than other existing methods (p<0.001). (b) The …
The x-axis represents different targets, and y-axis represents Cα-RMSD values. RMSD, root mean square deviation.
(a) Analysis of surface amino acids for predicted H3 loops. Y-axis represents average number of surface residues for H3 loops (n = 131). The surface residues of AF2 models are significantly higher …
The values represent the difference in SASA between H3 structures predicted by AF2 or H3-OPT and experimentally determined structures. Positive values indicate that the predicted structures have …
(a) Performance of H3-OPT in binding site prediction. comparison of prediction accuracy between H3-OPT and AF2 for antibody–antigen binding sites (n = 27). Box represents interquartile range (IQR); …
PDB ID | Ranked 0 RMSD | Lowest energy RMSD | Lowest RMSD | ΔRMSD* | ||
---|---|---|---|---|---|---|
4kmt | 1.06 | 1.14 | 1.05 | –0.08 | ||
5i19 | 2.16 | 1.91 | 1.77 | 0.25 | ||
5i1l | 3.80 | 3.20 | 3.19 | 0.60 | ||
5i17 | 2.86 | 3.71 | 2.86 | –0.85 | ||
5i1d | 2.10 | 2.10 | 2.02 | 0.00 | ||
5i1c | 2.43 | 1.66 | 1.45 | 0.77 | ||
5i1a | 2.37 | 0.85 | 0.59 | 1.52 | ||
5i1i | 3.72 | 3.51 | 3.51 | 0.21 | ||
5i15 | 2.16 | 1.94 | 1.35 | 0.22 | ||
5i16 | 3.19 | 1.70 | 1.39 | 1.49 | ||
5i18 | 2.88 | 2.88 | 2.88 | 0.00 | ||
5i1e | 1.62 | 1.13 | 0.92 | 0.49 | ||
5i1g | 2.08 | 2.08 | 2.00 | 0.00 | ||
5i1h | 1.58 | 1.84 | 1.32 | –0.26 |
ΔRMSD was calculated by subtracting the RMSD of predicted model from the RMSD of Ranked_0 model.
Method | Freeze terminal Cα | CDR* | Phase | Ranked 0 RMSD | Lowest energy RMSD | Lowest RMSD | ΔRMSD |
---|---|---|---|---|---|---|---|
PM6D3 | Y | H3 | Gas | 2.64 | 2.76 | 2.16 | –0.12 |
PM6D3 | N | H3 | Gas | 2.53 | 2.67 | 2.03 | –0.14 |
PM6D3 | N | H1, H2, H3 | Gas | 2.50 | 2.64 | 2.00 | –0.14 |
B3LYP | N | H3 | Gas | 2.66 | 2.87 | 2.30 | –0.21 |
B3LYP | N | H3 | Water | 2.66 | 2.68 | 2.30 | –0.02 |
RMSD = root mean square deviation.
CDR means the energy of which loop is used to re-rank AF2 models.
Method | Freeze terminal Cα | Structure generation method | Phase | Ranked 0 RMSD | Lowest energy RMSD/opted RMSD | Lowest RMSD | ΔRMSD |
---|---|---|---|---|---|---|---|
PM6D3 | Y | / | Gas | 1.69 | 1.74/1.87 | 1.37 | –0.05 |
B3LYP | N | / | Gas | 1.63 | 1.65/2.55 | 1.38 | –0.02 |
B3LYP | N | / | Water | 1.63 | 1.58/2.25 | 1.38 | 0.05 |
B3LYP | N | Boltzmann | Gas | 1.56 | 2.05 | 1.28 | –0.49 |
B3LYP | N | Boltzmann | Water | 1.56 | 1.81 | 1.28 | –0.25 |
B3LYP | N | Boltzmann, minimized | Gas | 1.56 | 1.96 | 1.28 | –0.40 |
B3LYP | N | Boltzmann, minimized | Water | 1.56 | 1.84 | 1.28 | –0.28 |
RMSD = root mean square deviation.
PDB ID | Cα-RMSDRanked_0 | Cα-RMSDMD_opt | ΔCα-RMSD |
---|---|---|---|
7n0r | 10.92 | 5.62 ± 0.97 | 5.30 |
3juy | 6.37 | 5.71 ± 0.23 | 0.66 |
5y80 | 6.61 | 7.59 ± 0.47 | –0.98 |
7a4t | 6.19 | 7.48 ± 0.29 | –1.29 |
4nzr | 6.57 | 7.73 ± 0.26 | –1.16 |
6xzu | 7.45 | 6.34 ± 0.94 | 1.11 |
6x05 | 6.32 | 7.48 ± 0.63 | –1.16 |
3c08 | 6.68 | 7.01 ± 0.11 | –0.33 |
4z9k | 9.04 | 8.01 ± 0.37 | 1.03 |
6oca | 7.61 | 8.01 ± 0.34 | –0.40 |
RMSD = root mean square deviation.
RMSDCα (Å) | |
---|---|
H3-OPT | 2.24 ± 1.05 |
AF2 | 2.85 ± 0.69 |
ESM2 | 2.31 ± 1.13 |
Without PLM | 2.41 ± 1.26 |
AntiBERTy | 2.49 ± 1.42 |
ProtTrans-T5 | 2.40 ± 1.28 |
RMSD = root mean square deviation.
PDB ID | AF2 (kcal/mol) | AF2 RMSDCα (Å) | H3-OPT (kcal/mol) | H3-OPT RMSDCα (Å) | AF2 (kcal/mol) | H3-OPT (kcal/mol) | |||||
---|---|---|---|---|---|---|---|---|---|---|---|
MM/GBSA | MM/PBSA | MM/GBSA | MM/PBSA | |ΔMM/GBSA*| | |ΔMM/PBSA| | |ΔMM/GBSA| | |ΔMM/PBSA| | ||||
2ghw | –29.20 | –33.36 | 2.7 | –14.70 | –21.36 | 3.0 | 8.63 | 2.42 | 23.13 | 14.42 | |
2yc1 | –38.85 | –37.73 | 2.3 | –43.80 | –48.72 | 1.5 | 6.80 | 18.67 | 1.85 | 7.68 | |
3l95 | –29.59 | –53.35 | 2.5 | –47.22 | –68.86 | 2.5 | 23.60 | 11.44 | 5.97 | 4.07 | |
3u30 | –37.31 | –42.41 | 2.6 | –44.94 | –50.07 | 2.5 | 9.64 | 2.18 | 2.01 | 5.48 | |
4cni | –36.96 | –42.93 | 1.0 | –31.92 | –40.39 | 1.3 | 8.54 | 7.44 | 3.50 | 4.89 | |
4nbz | –36.59 | –43.79 | 1.9 | –59.61 | –54.23 | 0.6 | 10.17 | 3.30 | 12.85 | 13.74 | |
4xnq | –13.55 | –17.47 | 2.7 | –31.51 | –30.94 | 0.5 | 15.40 | 12.32 | 2.57 | 1.15 | |
4ydl | –52.51 | –74.25 | 4.8 | –49.17 | –73.57 | 3.6 | 6.82 | 6.53 | 10.15 | 7.21 | |
5e5m | –59.72 | –71.15 | 3.0 | –41.29 | –53.70 | 7.3 | 0.50 | 5.79 | 18.93 | 11.66 | |
5f7y | –61.76 | –69.46 | 2.7 | –60.33 | –69.43 | 1.4 | 3.95 | 6.38 | 5.38 | 6.41 | |
6kyz | –12.66 | –20.32 | 4.0 | –9.36 | –17.13 | 3.7 | 17.63 | 17.21 | 20.93 | 20.40 | |
6o9h | –39.53 | –43.45 | 2.8 | –52.27 | –57.51 | 0.6 | 10.45 | 13.31 | 2.29 | 0.74 | |
6pyd | –45.87 | –58.71 | 1.0 | –35.75 | –45.28 | 1.1 | 6.29 | 13.50 | 3.83 | 0.06 | |
6u9s | –36.54 | –48.66 | 1.0 | –39.79 | –44.80 | 1.3 | 14.35 | 10.42 | 11.11 | 14.28 | |
Average | / | / | 2.6 | / | / | 2.4 | 10.20 | 9.35 | 8.89 | 8.01 |
ΔMM/GBSA (or ΔMM/PBSA) was calculated by subtracting the MM/GBSA (or MM/PBSA) of predicted model from the MM/GBSA· (or MM/PBSA) of experimental structure.
Nres is the number of residues (Jumper et al., 2021).
Feature and shape | Description |
---|---|
Amino acid type [Nres, 21] | One-hot representation of the input amino acid sequence (including 20 amino acids and unknown). |
3D coordinates [Nres, 3] | Cα coordinates of all AlphaFold2-predicted residues |
Backbone torsion angles [Nres, 6] | Sine and cosine encoding of all predicted three backbone torsion angles. |
Torsion angles mask [Nres, 3] | A mask indicating if the angle was presented in the predicted structure. |
H3 residue mask [Nres, 1] | A mask indicating if the residue was located in H3 loop. |
Pairwise distances [Nres, Nres, 39] | One hot representation of residue alpha carbon atoms distance. The pairwise distances ranging from 3.25 Å to 50.75 Å were put into 38 bins equally and the last bin contained any larger distances. |
Pairwise amino acid type [Nres, Nres, 21] | One-hot representation of the input amino acid sequence. |
Model | 2 | 5 | 1 | 3 | Best |
---|---|---|---|---|---|
Initial learning rate | 1–4 | 5–4 | 1–3 | 5–4 | 1–4 |
Hidden layers | 64 | 64 | 64 | 64 | 64 |
Iterations numbers of Evoformer-like layer | 6 | 6 | 4 | 4 | 4 |
Average RMSDCα (Å) | 2.42 | 2.36 | 2.35 | 2.33 | 2.24 |
RMSD = root mean square deviation.
Cutoff | Cα-RMSD (Å) |
---|---|
0.70 | 2.46 |
0.75 | 2.30 |
0.80 | 2.24 |
0.85 | 2.17 |
0.90 | 2.29 |
0.95 | 2.28 |
RMSD = root mean square deviation.
PDBID | AF2(kcal//mol) | AF2 RMSD_(Cu) (A) | H3-OPT(kcal//mol) | AF2(kcal//mol) | H3-OPT(kcal//mol) | |||||
---|---|---|---|---|---|---|---|---|---|---|
MM/ GBSA | MM/ PBSA | MM/ GBSA | MM/ PBSA | ("Å") | |/_\MM//GBSA^(**)| | | /_\MM//PBSA∣ | [ /_\MM//GBSA] | |/_\MM//PBSA| | ||
2ghw | -29.20 | -33.36 | 2.7 | -14.70 | -21.36 | 3.0 | 8.63 | 2.42 | 23.13 | 14.42 |
2yc1 | -38.85 | -37.73 | 2.3 | -43.80 | -48.72 | 1.5 | 6.80 | 18.67 | 1.85 | 7.68 |
3195 | -29.59 | -53.35 | 2.5 | -47.22 | -68.86 | 2.5 | 23.60 | 11.44 | 5.97 | 4.07 |
3u30 | -37.31 | -42.41 | 2.6 | -44.94 | -50.07 | 2.5 | 9.64 | 2.18 | 2.01 | 5.48 |
4cni | -36.96 | -42.93 | 1.0 | -31.92 | -40.39 | 1.3 | 8.54 | 7.44 | 3.50 | 4.89 |
4nbz | -36.59 | -43.79 | 1.9 | -59.61 | -54.23 | 0.6 | 10.17 | 3.30 | 12.85 | 13.74 |
4xx nq | -13.55 | -17.47 | 2.7 | -31.51 | -30.94 | 0.5 | 15.40 | 12.32 | 2.57 | 1.15 |
4ydl | -52.51 | -74.25 | 4.8 | -49.17 | -73.57 | 3.6 | 6.82 | 6.53 | 10.15 | 7.21 |
5e5m | -59.72 | -71.15 | 3.0 | -41.29 | -53.70 | 7.3 | 0.50 | 5.79 | 18.93 | 11.66 |
577 y | -61.76 | -69.46 | 2.7 | -60.33 | -69.43 | 1.4 | 3.95 | 6.38 | 5.38 | 6.41 |
6kyz | -12.66 | -20.32 | 4.0 | -9.36 | -17.13 | 3.7 | 17.63 | 17.21 | 20.93 | 20.40 |
609h | -39.53 | -43.45 | 2.8 | -52.27 | -57.51 | 0.6 | 10.45 | 13.31 | 2.29 | 0.74 |
6pyd | -45.87 | -58.71 | 1.0 | -35.75 | -45.28 | 1.1 | 6.29 | 13.50 | 3.83 | 0.06 |
6u9s | -36.54 | -48.66 | 1.0 | -39.79 | -44.80 | 1.3 | 14.35 | 10.42 | 11.11 | 14.28 |
Average | 1 | I | 2.6 | l | 1 | 2.4 | 10.20 | 9.35 | 8.89 | 8.01 |