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Protein complex structure — a mmCIF (
.cif / .mmcif)
or PDB (.pdb) file for the protein complex of interest.
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Protein A ID — identifier for the protein in chain A.
Can be a UniProt accession, gene name, or any alphanumeric label.
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Protein B ID — identifier for the protein in chain B.
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Variants — a tab-separated list of missense variants.
Chain assignment: Protein A must correspond to chain A in your structure
file, and Protein B to chain B. If they are reversed, swap your Protein A and Protein B
labels accordingly.
Variant format
Three tab-separated columns per line, no header row:
MUTATED_PROTEIN_ID VARIANT PARTNER_ID
- Column 1: ID of the protein carrying the mutation (must be Protein A or B).
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Column 2: Missense variant in single-letter notation —
[WT residue][1-based position][MT residue].
Example: V123A (Val→Ala at position 123).
Only the standard 20 amino acids are supported.
- Column 3: ID of the interaction partner (the other protein).
Position numbering: Positions are 1-based indices counting sequentially
through the residues present in the structure file (first residue in the structure = 1).
For AlphaFold3 outputs these match canonical sequence positions.
For PDB structures with missing or non-sequentially numbered residues, the position in
the variant notation should reflect the order of residues in the uploaded file, which
may differ from the PDB residue numbers or UniProt canonical positions.
After uploading a structure, the page shows the number of residues in each chain to
help you verify the numbering.
Example
O00548 A653T P46531
O00548 R661S P46531
O00548 N34I P46531
P46531 W89R O00548
P46531 E100K O00548
The first three rows specify mutations on Protein A (O00548).
The last two rows specify mutations on Protein B (P46531)
— note that the mutated protein is listed first.
Obtaining a structure file
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AlphaFold3 Server —
alphafoldserver.com
generates predicted complex structures in mmCIF format.
AlphaFold3 outputs are subject to Google DeepMind’s
Output Terms of Use (non-commercial use only).
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Protein Data Bank —
experimental structures from rcsb.org
in mmCIF or PDB format.
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Other prediction tools — AlphaFold-Multimer, RoseTTAFold,
or any tool producing mmCIF or PDB output.
The structure must contain chains labeled A and B.
Output
A tab-separated file with one row per variant:
complex_id variant score
O00548_P46531 A653T 0.0852
O00548_P46531 R661S 0.0680
O00548_P46531 N34I 0.3541
complex_id: underscore-joined protein IDs (mutated protein first)variant: variant notation as provided-
score: predicted probability of interaction disruption (0–1).
Scores ≥ 0.5 indicate predicted disruption.