AlphaFold-predicted structures of IL-6 dimers

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