Published July 15, 2024
| Version v1
Dataset
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AlphaFold-predicted structures of IL-6 dimers
Authors/Creators
Description
1. Pre-processed files
2. Processed files:
- CIF files from AF3 were converted to PDB format
- only C_alpha atoms were kept
- polyG linkers were deleted and chain IDs for the second part were renamed to "B"
- chain "A" was aligned to reference structure using the non-swapped amino acids
- the models were classified into "non-swapped", "swapped" and "other"
| # | Approach | Weights name | Templates | Dropout | N_models (different weights) | N_runs (different seeds) |
| 1 | AlphaFold 2.3.2 as a monomer with 50×Gly linker | monomer_ptm | Y | N | 5 | 5 |
| 2 | monomer_ptm | N | N | 5 | 5 | |
| 3 | ColabFold 1.5.5 as a monomer with 50×Gly linker | alphafold2_ptm | Y | Y | 5 | 5 |
| 4 | alphafold2_ptm | Y | N | 5 | 5 | |
| 5 | alphafold2_ptm | N | Y | 5 | 5 | |
| 6 | alphafold2_ptm | N | N | 5 | 5 | |
| 7 | AlphaFold 2.3.2 as a dimer | multimer | Y | N | 5 | 5 |
| 8 | multimer | N | N | 5 | 5 | |
| 9 | ColabFold 1.5.5 as a dimer | alphafold2_multimer_v3 | Y | Y | 5 | 5 |
| 10 | alphafold2_multimer_v3 | Y | N | 5 | 5 | |
| 11 | alphafold2_multimer_v3 | N | Y | 5 | 5 | |
| 12 | alphafold2_multimer_v3 | N | N | 5 | 5 | |
| 13 | AlphaFold3 as a monomer with 50×Gly linker | Default (accessed on 24.06.2024) | 5 | 20 | ||
| 14 | AlphaFold3 as a dimer | Default (accessed on 24.06.2024) | 5 | 20 | ||
| 15 | SPEACH_AF | alphafold2_ptm | N | N | 5 | 5 |
Files
Pre-processed files.zip
Files
(172.2 MB)
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