ArticleBioinformatics (Oxford, England)2025
AF3Complex yields improved structural predictions of protein complexes.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- TINA: a geometry-aware post-hoc scoring framework for protein-protein interaction.Acta pharmacologica Sinica · 2026Article
- PrePPI - Structure-based Prediction of Protein-protein Interactomes and Networks.Journal of molecular biology · 2026Article
- Toward mechanistic virtual immune cells.Nature biotechnology · 2026Article
- AlphaInterp: Mechanistic Interpretability of AlphaFold 3 Reveals How Evolutionary Information Shapes Protein Structure Prediction.bioRxiv : the preprint server for biology · 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
- Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks.Nature communications · 2026Article
- GlueFinder: A Data-Driven Framework for the Rational Discovery of Molecular Glues.Journal of chemical information and modeling · 2026Article
- Practical Outcomes From CASP16 for Users in Need of Biomolecular Structure Prediction.Proteins · 2026Review
- Know your scientist: KYC as biosecurity infrastructure.Frontiers in microbiology · 2026Article
- Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design.Computational and structural biotechnology journal · 2026Article
- SurfDiff: protein surface profiling for selective or broadly reactive epitope prioritisation in binder and immunogen design.bioRxiv : the preprint server for biology · 2025Article
- GlueFinder: A Data-Driven Framework for the Rational Discovery of Molecular Glues.bioRxiv : the preprint server for biology · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
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2 authors.
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Abstract
motivationAccurate structures of protein complexes are essential for understanding biological pathway function. A previous study showed how downstream modifications to AlphaFold 2 could yield AF2Complex, a model better suited for protein complexes. Here, we introduce AF3Complex, a model equipped with both similar and novel improvements, built on AlphaFold 3.
resultsBenchmarking AF3Complex and AlphaFold 3 on a large dataset of protein complexes, it was shown that AF3Complex outperforms AlphaFold 3. Moreover, by evaluating the structures generated by AF3Complex on datasets of protein-peptide complexes and antibody-antigen complexes, it was established that AF3Complex could create high-fidelity structures for these challenging complex types. Additionally, when deployed to generate structural predictions for protein complexes used in the recent CASP16 competition, AF3Complex yielded structures that would have placed it among the top models in the competition. AVAILABILITY AND IMPLEMENTATION: The AF3Complex code is freely available at https://github.com/Jfeldman34/AF3Complex.git.
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