Predict the effect of missense variants on protein–protein interactions

MutPred-PPI predicts whether a missense variant disrupts a specific protein–protein interaction from the three-dimensional structure of the complex.

Submit a prediction Help & format About

Stewart R, Laval F, Coppin G, Spirohn-Fitzgerald K, Tixhon M, Hao T, Calderwood MA, Mort M, Cooper DN, Vidal M, Radivojac P. Predicting interaction-specific protein-protein interaction perturbations by missense variants with MutPred-PPI. The 30th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2026. Available on bioRxiv 2025.12.20.695738.

Submit a prediction job

Upload a protein complex structure and a list of missense variants to predict interaction disruption. Up to 100 variants per job. Input format guide →

Upload the mmCIF or PDB structure file for the protein complex. Protein A must correspond to chain A, Protein B to chain B. AlphaFold3 structures can be generated at alphafoldserver.com (subject to Google DeepMind Output Terms of Use).

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Drag & drop your .cif, .mmcif, or .pdb file here,
or click to browse

Identifier for the protein in chain A.

Identifier for the protein in chain B.

One variant per line, three columns: MUTATED_PROTEIN_ID  VARIANT  PARTNER_ID
Columns may be separated by tabs or spaces. Variant notation: WT residue + 1-based position + MT residue (e.g. V123A). To specify a mutation on Protein B, list Protein B first. See examples

⇩ Drop a variants file here or browse