Tom Goddard
July 11, 2025
These are prediction times for running Boltz versions 2.1.1, 1.0.0 and 0.4.1 using ChimeraX for PDB structures of different sizes and with different Boltz options.
Boltz prediction times in minutes. Failures report out of memory.
| PDB code | Tokens | Mac M1 16 GB | Mac M1 Max 32 GB | Mac M2 Ultra 64 GB | Linux i9 CPU 64 GB | Linux Nvidia 4090 16-bit | Linux Nvidia 4090 32-bit | Windows i7 CPU 64 GB | Windows Nvidia 3070 16-bit | Windows Nvidia 3070 32-bit | Windows Nvidia 4070 32-bit | Number of residues and atoms and prediction error |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 8rf4 | 129 | 1.2 b2 1.4 b1 1.7 b0 3.4 b2s 3.9 b1s 3.7 b2a | 0.8 b2 1.0 b1 0.9 b0 2.5 b2s 1.8 b2a | 0.8 b2 0.9 b1 0.8 b0 2.1 b2s 1.5 b2a | 1.1 b2 1.2 b1 2.3 b2s 3.7 b2a | 0.3 b2 0.4 b1 0.5 b1s 0.6 b2a | 0.4 b1 0.5 b0 0.5 b1s | 2.0 b2 2.2 b1 2.2 b0 3.1 b1s 6.2 b2a | 0.8 b2 1 b1 1.8 b2a | 1 b1 1 b0 1.2 b1s | 1.6 b0 | 118 amino acids, 11 ligand atoms, 0.8A RMSD 108 residues |
| 1hho | 382 | fail b2 fail b1 fail b0 fail b2 1‑heme fail b1 1‑heme 7 b0 1‑heme fail b2 no ligands 4.2 b1 no ligands | 1.5 b2 1.9 b1 2.1 b0 6.7 b2s | 1.4 b2 1.3 b1 1.4 b0 3.8 b2s 3.4 b1s | 8.0 b2 8.4 b1 11 b2s | 0.5 b2 0.6 b1 0.7 b1s | 0.6 b1 0.8 b0 0.8 b1s | 11 b2 11 b1 12 b0 15 b1s | 2.0 b2 1.9 b1 2.3 b1s | 4.8 b1 5 b0 5.3 b1s | 4 b0 | 287 amino acids, 95 ligand atoms, 0.4A RMSD 146 residues |
| 9moj | 660 | 18 b2 17 b1 fail b0 30 b2s 29 b1s | 3.8 b2 3.7 b1 3.9 b0 7.3 b2s | 2.3 b2 2.2 b1 2.5 b0 3.7 b2s 3.5 b1s | 24 b2 23 b1 34 b2s | 0.6 b2 0.7 b1 1.0 b1s | 0.9 b1 1.2 b0 1.2 b1s | 29 b2 27 b1 29 b0 | 2.5 b2 2.5 b1 3.6 b1s | 7.1 b1 7 b0 8.2 b1s | 3.2 b0 | 660 amino acids, heterotetramer, 0.8A RMSD 132 residues |
| 9h1k | 671 | 23 b2 22 b1 | 4.9 b2 4.3 b1 4.6 b0 11 b2s | 2.7 b2 2.5 b1 2.7 b0 5.6 b2s 4.9 b1s | 29 b2 27 b1 39 b2s | 0.7 b2 0.8 b1 1.1 b1s | 1.1 b1 1.5 b0 1.4 b1s | 38 b2 31 b1 32 b0 | 9.5 b2 7.7 b1 9.3 b1s | 17 b1 17 b0 20 b1s | 27 b0 | 560 amino acids, 59 rna bases, 52 ligand atoms, 0.7A RMSD protein, RNA wrong |
| 9b3h | 911 | fail b2 44 b1 | 10 b2 11 b1 17 b0 15 b2s | 5.1 b2 4.4 b1 4.7 b0 6.9 b2s 5.9 b1s | 60 b2 56 b1 75 b2s | 1.1 b2 1.3 b1 1.7 b1s | 1.7 b1 2.7 b0 2.1 b1s | 67 b1 96 b0 | 28 b2 28 b1 | 80 b2 48 b1 49 b0 | 75 b0 | 911 amino acids, heterodimer, 1A RMSD 509 residues |
| 9fz5 | 1025 | fail b1 | 13 b2 12 b1 15 b0 18 b2s | 7.0 b2 5.8 b1 6.6 b0 9.1 b2s 7.9 b1s | 82 b2 78 b1 100 b2s | 1.3 b2 1.7 b1 1.7 b0 2.0 b1s | fail b1 fail b0 fail b1s | 40 b2 40 b1 | 1025 amino acids, heterotrimer, 3.7A RMSD 740 residues | |||
| 9mcw | 1154 | fail b1 | 18 b2 >47 b1 13 b0 fail b2s | 7.2 b2 6.8 b1 6.8 b0 fail b2s fail b1s | 96 b2 91 b1 175 b2s | 1.4 b2 1.7 b1 2.0 b1s | 2.5 b1 4.4 b0 fail b1s | 54 b2 | 1154 rna bases, homodimer, wrong dimer and monomer conformations | |||
| 8sa0 | 1371 | 28 b2 25 b1 fail b0 fail b2s 146 b2a | 38 b2 12 b1 23 b0 41 b2s 17 b1s 34 b2a | 164 b2 151 b1 186 b2s 171 b2a | fail b2 2.4 b1 2.4 b0 3.0 b1s | fail b1 fail b0 | 1274 amino acids, 97 ligand atoms, 3.4A RMSD 1151 residues | |||||
| 9gh4 | 1467 | 32 b2 | 41 b2 172 b1 | 188 b2 | 2.1 b2 fail b1 fail b0 | Protein homotrimer, monomer 489 residues, 1.1A RMSD for 750 residues |