Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation

Chop Yan Lee, Dalmira Hubrich, Julia K. Varga, Christian Schäfer, Mareen Welzel, Eric Schumbera, Milena Djokic, Joelle M. Strom, Jonas Schönfeld, Johanna L. Geist, Feyza Polat, Toby J. Gibson, Claudia Isabelle Keller Valsecchi, Manjeet Kumar, Ora Schueler-Furman*, Katja Luck*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Structural resolution of protein interactions enables mechanistic and functional studies as well as interpretation of disease variants. However, structural data is still missing for most protein interactions because we lack computational and experimental tools at scale. This is particularly true for interactions mediated by short linear motifs occurring in disordered regions of proteins. We find that AlphaFold-Multimer predicts with high sensitivity but limited specificity structures of domain-motif interactions when using small protein fragments as input. Sensitivity decreased substantially when using long protein fragments or full length proteins. We delineated a protein fragmentation strategy particularly suited for the prediction of domain-motif interfaces and applied it to interactions between human proteins associated with neurodevelopmental disorders. This enabled the prediction of highly confident and likely disease-related novel interfaces, which we further experimentally corroborated for FBXO23-STX1B, STX1B-VAMP2, ESRRG-PSMC5, PEX3-PEX19, PEX3-PEX16, and SNRPB-GIGYF1 providing novel molecular insights for diverse biological processes. Our work highlights exciting perspectives, but also reveals clear limitations and the need for future developments to maximize the power of Alphafold-Multimer for interface predictions.

Original languageAmerican English
Pages (from-to)75-97
Number of pages23
JournalMolecular Systems Biology
Issue number2
StatePublished - 2 Feb 2024

Bibliographical note

Publisher Copyright:
© The Author(s) 2024.


  • AlphaFold
  • Benchmarking
  • Experimental Validation
  • Linear Motifs
  • Protein Interaction Interface Prediction


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