ArticleNature methods2024
CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 69 citations in OpenAlex.
- Evaluation of methods for AlphaFold-based integrative modeling.bioRxiv : the preprint server for biology · 2026Article
- A functional atlas of transposon-encoded products and their integration into host networks.Nature communications · 2026Article
- Reconstructing the evolutionary origin of β-catenin recognition in the Wnt destruction complex.Molecular biology and evolution · 2026Article
- Stoic: fast and accurate protein stoichiometry prediction.Bioinformatics (Oxford, England) · 2026Article
- When can AlphaFold predict the oligomeric states of proteins?Protein science : a publication of the Protein Society · 2026Article
- Computational Design and Biopharmaceutical Evaluation of a Chimeric Nanoparticle Vaccine for Targeted Delivery against BK Polyomavirus.Pharmaceutical research · 2026Article
- Integrating AlphaFold2, RoseTTAFold2, and HADDOCK to refine Protein-Protein Interaction (PPI) candidate selection: A case study with ZWINT.Biochemistry and biophysics reports · 2026Article
- Computational prediction resolves thousands of homooligomeric phage protein structures.bioRxiv : the preprint server for biology · 2026Article
- PreStoi allows accurate prediction of protein complex stoichiometry by integrating AlphaFold3 and template information.Communications biology · 2026Article
- Atlas of predicted protein complex structures across kingdoms.Nature communications · 2026Article
- Positive Selection Targeted Primate Genes that Encode Transposable Element Repressors.Genome biology and evolution · 2026Article
- Self-assembling protein cages: from coiled-coil module to machine learning-drivenMaterials advances · 2026Review
- Measuring and locating the changes in protein structure using MELO.Nature communications · 2026Article
- Discovery of a fungal Tc toxin complex and functional mycoserpin through a novel two-by-two comparative genomics approach.Frontiers in cellular and infection microbiology · 2026Article
- A CSGNN model-based method for essential protein identification.Frontiers in bioinformatics · 2026Article
- A guide to building the matrisome interactome: from computational predictions to experimental validation.The FEBS journal · 2026Review
- Cysteine-enabled cleavability to advance cross-linking mass spectrometry for global analysis of endogenous protein-protein interactions.Nature communications · 2025Article
- Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations.Communications chemistry · 2025Article
- State-of-the-Art and Future Directions in Structural Proteomics.Molecular & cellular proteomics : MCP · 2025Review
- gapTrick-structural characterization of protein-protein interactions using AlphaFold.Bioinformatics (Oxford, England) · 2025Article
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2 authors at 1 institution in 1 country.
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Abstract
Deep learning models, such as AlphaFold2 and RosettaFold, enable high-accuracy protein structure prediction. However, large protein complexes are still challenging to predict due to their size and the complexity of interactions between multiple subunits. Here we present CombFold, a combinatorial and hierarchical assembly algorithm for predicting structures of large protein complexes utilizing pairwise interactions between subunits predicted by AlphaFold2. CombFold accurately predicted (TM-score >0.7) 72% of the complexes among the top-10 predictions in two datasets of 60 large, asymmetric assemblies. Moreover, the structural coverage of predicted complexes was 20% higher compared to corresponding Protein Data Bank entries. We applied the method on complexes from Complex Portal with known stoichiometry but without known structure and obtained high-confidence predictions. CombFold supports the integration of distance restraints based on crosslinking mass spectrometry and fast enumeration of possible complex stoichiometries. CombFold's high accuracy makes it a promising tool for expanding structural coverage beyond monomeric proteins.
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