{"id":"https://openalex.org/W4416714296","doi":"https://doi.org/10.1038/s42004-025-01763-0","title":"Challenging AlphaFold in predicting proteins with large-scale allosteric transitions","display_name":"Challenging AlphaFold in predicting proteins with large-scale allosteric transitions","publication_year":2025,"publication_date":"2025-11-26","ids":{"openalex":"https://openalex.org/W4416714296","doi":"https://doi.org/10.1038/s42004-025-01763-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/41299000","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/12658248"},"language":"en","primary_location":{"id":"doi:10.1038/s42004-025-01763-0","doi":"https://doi.org/10.1038/s42004-025-01763-0","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42004-025-01763-0","pdf_url":"https://www.nature.com/articles/s42004-025-01763-0.pdf","source":{"id":"https://openalex.org/S4210191625","display_name":"Communications Chemistry","issn_l":"2399-3669","issn":["2399-3669"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","jufo-1","ki-jl-1","norway-1","oarl","poland-20","russia-white-list-1"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Communications Chemistry","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.nature.com/articles/s42004-025-01763-0.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5120667320","display_name":"Brooks H. Perkins-Jechow","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Brooks H. Perkins-Jechow","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120431461","display_name":"Juan Pablo Iglesias Ahualli","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Juan Pablo Iglesias Ahualli","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120521402","display_name":"Huyen Thuc Nhu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Huyen Thuc Nhu","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105965148","display_name":"Alireza Omidi","orcid":"https://orcid.org/0000-0003-3598-9480","observed_orcids":["https://orcid.org/0000-0003-3598-9480"]},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Alireza Omidi","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada"],"raw_orcid":"https://orcid.org/0000-0003-3598-9480","affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Chunchao Li","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Chunchao Li","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012265264","display_name":"Jorge A. Holguin-Cruz","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jorge A. Holguin-Cruz","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Daeahn Cho","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I67900169","display_name":"Chung-Ang University","ror":"https://ror.org/01r024a98","country_code":"KR","type":"education","lineage":["https://openalex.org/I67900169"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Daeahn Cho","raw_affiliation_strings":["School of Integrative Engineering, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Integrative Engineering, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I67900169"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081482117","display_name":"Dokyun Na","orcid":"https://orcid.org/0000-0002-9107-7040","observed_orcids":["https://orcid.org/0000-0002-9107-7040","https://orcid.org/0000-0002-0423-2015"]},"institutions":[{"id":"https://openalex.org/I67900169","display_name":"Chung-Ang University","ror":"https://ror.org/01r024a98","country_code":"KR","type":"education","lineage":["https://openalex.org/I67900169"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Dokyun Na","raw_affiliation_strings":["School of Integrative Engineering, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Integrative Engineering, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I67900169"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013572921","display_name":"Nawar Malhis","orcid":"https://orcid.org/0000-0002-1317-833X","observed_orcids":["https://orcid.org/0000-0002-1317-833X"]},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nawar Malhis","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada"],"raw_orcid":"https://orcid.org/0000-0002-1317-833X","affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110563086","display_name":"Jennifer M. Bui","orcid":"https://orcid.org/0009-0004-4861-3778","observed_orcids":["https://orcid.org/0009-0004-4861-3778"]},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jennifer M. Bui","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011423412","display_name":"J\u00f6rg A. Gsponer","orcid":"https://orcid.org/0000-0003-3672-6594","observed_orcids":["https://orcid.org/0000-0003-3672-6594"]},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"J\u00f6rg Gsponer","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada. gsponer@msl.ubc.ca","Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada. gsponer@msl.ubc.ca","Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada"],"raw_orcid":"https://orcid.org/0000-0003-3672-6594","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada. gsponer@msl.ubc.ca","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada. gsponer@msl.ubc.ca","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5011423412"],"corresponding_institution_ids":["https://openalex.org/I141945490"],"apc_list":{"value":3690,"currency":"USD","value_usd":3690},"apc_paid":{"value":3690,"currency":"USD","value_usd":3690},"fwci":3.364,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.94228476,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"8","issue":"1","first_page":"378","last_page":"378"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0012000000569969416,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/alphafold2","display_name":"AlphaFold2","score":0.7459999918937683},{"id":"https://openalex.org/keywords/alphafold-3","display_name":"AlphaFold3","score":1.0},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"protein structure prediction","score":0.8389999866485596},{"id":"https://openalex.org/keywords/allosteric-transition","display_name":"allosteric transition","score":0.8949999809265137},{"id":"https://openalex.org/keywords/conformational-heterogeneity","display_name":"conformational heterogeneity","score":0.9259999990463257},{"id":"https://openalex.org/keywords/multidomain-proteins","display_name":"multidomain proteins","score":0.7710000276565552},{"id":"https://openalex.org/keywords/protein-energy-landscape","display_name":"protein energy landscape","score":0.6050000190734863},{"id":"https://openalex.org/keywords/benchmarking","display_name":"benchmarking","score":0.5149999856948853}],"concepts":[{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.7796000242233276},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5074999928474426},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.49140000343322754},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.477400004863739},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45410001277923584},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.44859999418258667},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44510000944137573},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41909998655319214},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.3901999890804291},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.375900000333786},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.3257000148296356},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3183000087738037},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29750001430511475},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27559998631477356},{"id":"https://openalex.org/C2988375501","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein stability","level":2,"score":0.26829999685287476},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.2578999996185303},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.257099986076355},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.2565000057220459}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1038/s42004-025-01763-0","doi":"https://doi.org/10.1038/s42004-025-01763-0","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42004-025-01763-0","pdf_url":"https://www.nature.com/articles/s42004-025-01763-0.pdf","source":{"id":"https://openalex.org/S4210191625","display_name":"Communications Chemistry","issn_l":"2399-3669","issn":["2399-3669"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","jufo-1","ki-jl-1","norway-1","oarl","poland-20","russia-white-list-1"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Communications Chemistry","raw_type":"journal-article"},{"id":"pmid:41299000","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41299000","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Communications chemistry","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:902ea7adf8ba4c5fbaff4701eae6b9e0","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/902ea7adf8ba4c5fbaff4701eae6b9e0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Communications Chemistry, Vol 8, Iss 1, Pp 1-13 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1038/s42004-025-01763-0","doi":"https://doi.org/10.1038/s42004-025-01763-0","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42004-025-01763-0","pdf_url":"https://www.nature.com/articles/s42004-025-01763-0.pdf","source":{"id":"https://openalex.org/S4210191625","display_name":"Communications Chemistry","issn_l":"2399-3669","issn":["2399-3669"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","jufo-1","ki-jl-1","norway-1","oarl","poland-20","russia-white-list-1"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Communications Chemistry","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321487","display_name":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320331257","display_name":"Alliance de recherche num\u00e9rique du Canada","ror":"https://ror.org/010r6td27"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416714296.pdf","grobid_xml":"https://content.openalex.org/works/W4416714296.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W1482971402","https://openalex.org/W1589812083","https://openalex.org/W1964439982","https://openalex.org/W1975464455","https://openalex.org/W1995875735","https://openalex.org/W2011301426","https://openalex.org/W2015117663","https://openalex.org/W2035713281","https://openalex.org/W2042302972","https://openalex.org/W2062233810","https://openalex.org/W2066962978","https://openalex.org/W2071556670","https://openalex.org/W2072117460","https://openalex.org/W2076048958","https://openalex.org/W2091521837","https://openalex.org/W2096170764","https://openalex.org/W2114644515","https://openalex.org/W2114850508","https://openalex.org/W2121489662","https://openalex.org/W2125980227","https://openalex.org/W2138226825","https://openalex.org/W2141205833","https://openalex.org/W2145268834","https://openalex.org/W2154319440","https://openalex.org/W2156465034","https://openalex.org/W2156816941","https://openalex.org/W2158476854","https://openalex.org/W2163776261","https://openalex.org/W2508425869","https://openalex.org/W2740391153","https://openalex.org/W2780971412","https://openalex.org/W2803256436","https://openalex.org/W2950954328","https://openalex.org/W2972411752","https://openalex.org/W3003257820","https://openalex.org/W3035965352","https://openalex.org/W3107939614","https://openalex.org/W3128261063","https://openalex.org/W3138955974","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W4214847177","https://openalex.org/W4281790889","https://openalex.org/W4283326616","https://openalex.org/W4292636432","https://openalex.org/W4307844175","https://openalex.org/W4309506674","https://openalex.org/W4310159409","https://openalex.org/W4383957026","https://openalex.org/W4386793933","https://openalex.org/W4387204156","https://openalex.org/W4387599468","https://openalex.org/W4388627063","https://openalex.org/W4393233076","https://openalex.org/W4396723792","https://openalex.org/W4396895148","https://openalex.org/W4400353742","https://openalex.org/W4401844424","https://openalex.org/W4401895022","https://openalex.org/W4401978887","https://openalex.org/W4403728834","https://openalex.org/W4407722329","https://openalex.org/W4411887134","https://openalex.org/W4412165572"],"related_works":["https://openalex.org/W6942113326","https://openalex.org/W4225552973","https://openalex.org/W4416259908","https://openalex.org/W7166286863","https://openalex.org/W4392189384","https://openalex.org/W4401844424","https://openalex.org/W7130570881","https://openalex.org/W7203742510","https://openalex.org/W4408845504","https://openalex.org/W4382601731"],"abstract_inverted_index":{"Many":[0],"proteins":[1,42,148,182],"function":[2,149],"by":[3,142,150],"toggling":[4,151],"between":[5,47,152],"distinct":[6,153,188],"conformations,":[7,154,189],"yet":[8,120],"most":[9,155],"structure":[10,156],"predictors":[11,157],"have":[12],"been":[13],"trained":[14],"on":[15,32,177],"data":[16],"that":[17,43,55,97,192,205],"do":[18],"not":[19],"capture":[20,92,208],"this":[21],"conformational":[22,93,209],"diversity.":[23],"Here,":[24,165],"we":[25,95],"benchmarked":[26],"AlphaFold2,":[27,172],"AlphaFold3,":[28,173],"and":[29,49,114,174,190],"recent":[30,175],"variants":[31,176],"autoinhibited":[33,50,65,181,202],"proteins,":[34,66,203],"a":[35,161,178],"class":[36],"of":[37,63,82,106,127,137,171,180,200],"allosterically":[38],"regulated,":[39],"often":[40],"multi-domain":[41,84],"exist":[44],"in":[45,70],"equilibrium":[46],"active":[48],"states.":[51],"Our":[52],"analyses":[53],"show":[54,191],"AlphaFold2":[56,98,193],"fails":[57,194],"to":[58,91,123,160,195],"reproduce":[59,125,196],"the":[60,134,166,169,197],"experimental":[61,128,198],"structures":[62,140,199],"many":[64,147,201],"which":[67],"is":[68],"reflected":[69],"reduced":[71],"confidence":[72],"scores.":[73],"This":[74],"contrasts":[75],"sharply":[76],"with":[77,103],"its":[78,89],"high-accuracy,":[79],"high-confidence":[80],"predictions":[81],"non-autoinhibited":[83],"proteins.":[85],"When":[86],"tested":[87],"for":[88],"ability":[90],"diversity,":[94],"found":[96],"performs":[99],"better":[100],"when":[101,211],"combined":[102],"uniform":[104,213],"subsampling":[105],"sequence":[107,215],"alignments":[108],"rather":[109],"than":[110],"local":[111],"subsampling.":[112,217],"BioEmu":[113],"AlphaFold3":[115],"improve":[116],"upon":[117],"these":[118],"results,":[119],"still":[121],"struggle":[122],"accurately":[124],"details":[126],"structures.":[129],"Together,":[130],"our":[131],"study":[132],"underscores":[133],"persistent":[135],"challenges":[136],"predicting":[138],"protein":[139],"shaped":[141],"complex":[143],"energy":[144],"landscapes.":[145],"Although":[146],"remain":[158],"limited":[159],"single":[162],"static":[163],"fold.":[164],"authors":[167],"test":[168],"performance":[170],"dataset":[179],"exhibiting":[183],"at":[184],"least":[185],"two":[186],"functionally":[187],"but":[204],"it":[206],"can":[207],"diversity":[210],"using":[212],"multiple":[214],"alignment":[216]},"counts_by_year":[{"year":2026,"cited_by_count":14}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2025-11-27T00:00:00"}
