ArticleMolecular systems biology2024
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation.
Article in Molecular systems biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed, 77 citations in OpenAlex.
- Avl9 defines a family of DENN domain GTPase-activating proteins.The Journal of cell biology · 2026Article
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- Structures of dynamic interactors at native proteasomes by PhIX-MS and cryo-electron microscopy.Molecular cell · 2026Article
- Variant characterization in the intrinsically disordered human proteome.Nature structural & molecular biology · 2026Article
- From Thanatos to transcription: the emerging biology of THAP proteins.Cellular and molecular life sciences : CMLS · 2026Review
- SPPIDER-seq: sequence-based partner-aware predictor of protein-protein interaction sites.Bioinformatics (Oxford, England) · 2026Article
- Caveat emptor: predicting and modeling protein-DNA recognition and binding via machine-learning computational approaches.Nucleic acids research · 2026Review
- Navigating the uncharted: AI-driven advances in protein structure, dynamics, interactions and ligand interactions for understudied families.BioData mining · 2026Review
- Arabidopsis KASH domains are differentially required for distinct LINC complex roles in stomata, roots and pollen.Journal of cell science · 2026Article
- Systematic discovery of motif-based interactions of the auxiliary domains of USP family deubiquitinases.Nature communications · 2026Article
- SPPIDER-seq: Sequence-based partner-aware predictor of protein-protein interaction sites.bioRxiv : the preprint server for biology · 2026Article
- Alphafuser: a parsimonious approach to predicting higher-order protein complexes.Acta crystallographica. Section D, Structural biology · 2026Article
- AlphaFold-driven discovery of oxysterol-binding protein-related protein-phosphoinositide 3-, 4-, and 5-phosphatase interactions using new generation confidence scores.Protein science : a publication of the Protein Society · 2026Article
- Proteome-wide prediction of interactions between structured domains and peptide motifs reveals functionally coherent subnetworks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Hierarchical decoding of targeting tripeptide motif by the cytosolic iron-sulfur cluster assembly targeting complex.bioRxiv : the preprint server for biology · 2026Article
- A Survey of Predicted Protein-Protein Interactions Involving Disordered Regions in Humans.Journal of molecular biology · 2026Article
- From concept to application: Exploring the evolution and potential of DUBTAC technology.Acta pharmaceutica Sinica. B · 2026Review
- Vancomycin resistance in gram-positive infections: evolutionary strategies of survival.Archives of microbiology · 2026Review
- Competition between binding partners of yeast Pex3 affects peroxisome biology.The FEBS journal · 2026Article
- From Atoms to Cells: AI-Based Structure Prediction Fueling Molecular Dynamics Simulations in Computational Structural Biology.Advances in experimental medicine and biology · 2026Review
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 4 institutions in 2 countries.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.