{"doi":"10.1101/2023.06.22.546069","title":"Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>AlphaFold can predict the structures of monomeric and multimeric proteins with high accuracy but has a limit on the number of chains and residues it can fold. Here we show that a combination of AlphaFold and all-atom symmetric docking simulations enables highly accurate prediction of the structure of complex symmetrical assemblies. We present a method to predict the structure of complexes with cubic – tetrahedral, octahedral and icosahedral – symmetry from sequence. Focusing on proteins where AlphaFold can make confident predictions on the subunit structure, 21 cubic systems were assembled with a median TM-score of 0.99 and a DockQ score of 0.71. 15 had TM-scores of above 0.8 and were categorized as high-quality according to DockQ. The resulting models are energetically optimized and can be used for detailed studies of intermolecular interactions in higher-order symmetrical assemblies. The results demonstrate how explicit treatment of structural symmetry can significantly expand the size and complexity of AlphaFold predictions.</jats:p>","journal":null,"year":null,"id":626112,"datarank":0.26876392038420827,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.0,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":572357,"name":"Ingemar André","orcid":"0000-0002-4753-8233","position":1,"is_corresponding":false},{"id":1619507,"name":"Mads Jeppesen","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>AlphaFold can predict the structures of monomeric and multimeric proteins with high accuracy but has a limit on the number of chains and residues it can fold. Here we show that a combination of AlphaFold and all-atom symmetric docking simulations enables highly accurate prediction of the structure of complex symmetrical assemblies. We present a method to predict the structure of complexes with cubic – tetrahedral, octahedral and icosahedral – symmetry from sequence. Focusing on proteins where AlphaFold can make confident predictions on the subunit structure, 21 cubic systems were assembled with a median TM-score of 0.99 and a DockQ score of 0.71. 15 had TM-scores of above 0.8 and were categorized as high-quality according to DockQ. The resulting models are energetically optimized and can be used for detailed studies of intermolecular interactions in higher-order symmetrical assemblies. The results demonstrate how explicit treatment of structural symmetry can significantly expand the size and complexity of AlphaFold predictions.</jats:p>","is_dataset_classified":null,"base_score":1.791759469228055,"endowment":1.791759469228055,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19910364","pmcid":null,"openalex_id":"https://openalex.org/W4381952453","authors":[],"funders":[{"funder_name":"European Commission","grant_id":"771820","title":"Shape-directed protein assembly design"}],"total_grants":1,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2024,"count":3},{"year":2025,"count":1},{"year":2026,"count":1}],"oa_status":"green","license":"cc-by-nd","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2023/06/24/2023.06.22.546069.full.pdf","host_type":"repository"},{"url":"https://www.biorxiv.org/content/biorxiv/early/2023/06/24/2023.06.22.546069.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/2023.06.22.546069","host_type":"publisher"},{"url":"https://doi.org/10.1101/2023.06.22.546069","host_type":"repository"},{"url":"https://www.nature.com/articles/s41467-023-43681-6","host_type":"repository"},{"url":"https://doi.org/10.1038/s41467-023-43681-6","host_type":""},{"url":"https://dx.doi.org/10.5281/zenodo.8047513","host_type":""},{"url":"https://dx.doi.org/10.5281/zenodo.10116276","host_type":""},{"url":"http://dx.doi.org/10.5281/zenodo.10116276","host_type":""},{"url":"https://zenodo.org/records/10116276","host_type":""},{"url":"https://dx.doi.org/10.5281/zenodo.8047514","host_type":""},{"url":"http://dx.doi.org/10.5281/zenodo.8047514","host_type":""},{"url":"https://zenodo.org/records/8047514","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/38092742","host_type":""},{"url":"http://dx.doi.org/10.1038/s41467-023-43681-6","host_type":""},{"url":"https://doaj.org/article/c32293f70fa349b49ea2b1ef7b61e42f","host_type":""}],"fields_of_study":["Protein Structure and Dynamics","Enzyme Structure and Function","RNA and protein synthesis mechanisms","0206 medical engineering","02 engineering and technology"],"mesh_terms":[],"keywords":["Icosahedral symmetry","Docking (animal)","Tetrahedron","Crystallography","Octahedron","Monomer","Intermolecular force","Protein subunit","Chemistry","Chemical physics","Materials science","Physics","Computer science","Crystal structure","Molecule","Quantum mechanics","Protein Conformation","Science","Q","Proteins","Article"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-04T12:29:13.410357Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}