{"id":"https://openalex.org/W4394728357","doi":"https://doi.org/10.1146/annurev-biodatasci-102423-011435","title":"AlphaFold and Protein Folding: Not Dead Yet! The Frontier Is Conformational Ensembles","display_name":"AlphaFold and Protein Folding: Not Dead Yet! The Frontier Is Conformational Ensembles","publication_year":2024,"publication_date":"2024-04-11","ids":{"openalex":"https://openalex.org/W4394728357","doi":"https://doi.org/10.1146/annurev-biodatasci-102423-011435","pmid":"https://pubmed.ncbi.nlm.nih.gov/38603560","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/11892350"},"language":"en","primary_location":{"id":"doi:10.1146/annurev-biodatasci-102423-011435","doi":"https://doi.org/10.1146/annurev-biodatasci-102423-011435","is_oa":true,"landing_page_url":"https://doi.org/10.1146/annurev-biodatasci-102423-011435","pdf_url":null,"source":{"id":"https://openalex.org/S4210232080","display_name":"Annual Review of Biomedical Data Science","issn_l":"2574-3414","issn":["2574-3414"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","doyens","medline","norway-1","poland-20","russia-white-list-4"],"host_organization":"https://openalex.org/P4310320373","host_organization_name":"Annual Reviews","host_organization_lineage":["https://openalex.org/P4310320373"],"host_organization_lineage_names":["Annual Reviews"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Annual Review of Biomedical Data Science","raw_type":"journal-article"},"volume":null,"type":"review","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1146/annurev-biodatasci-102423-011435","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029297375","display_name":"Gregory R. Bowman","orcid":"https://orcid.org/0000-0002-2083-4892","observed_orcids":["https://orcid.org/0000-0002-2083-4892"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gregory R. Bowman","raw_affiliation_strings":["Departments of Biochemistry and Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA; email: grbowman@seas.upenn.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biochemistry and Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA; email: grbowman@seas.upenn.edu","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5029297375"],"corresponding_institution_ids":["https://openalex.org/I79576946"],"apc_list":null,"apc_paid":null,"fwci":1.3769,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.81648833,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"7","issue":"1","first_page":"51","last_page":"57"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/alphafold","display_name":"AlphaFold","score":0.9559999704360962},{"id":"https://openalex.org/keywords/protein-folding","display_name":"protein folding","score":0.9950000047683716},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"protein structure prediction","score":0.8309999704360962},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"conformational ensembles","score":0.9900000095367432},{"id":"https://openalex.org/keywords/protein-dynamics","display_name":"protein dynamics","score":0.9750000238418579},{"id":"https://openalex.org/keywords/protein-design","display_name":"protein design","score":0.6110000014305115},{"id":"https://openalex.org/keywords/drug-design","display_name":"drug design","score":0.8960000276565552}],"concepts":[{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5455341935157776},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44484785199165344},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4160420596599579},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4039229452610016},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3749149739742279},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.21584859490394592},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1146/annurev-biodatasci-102423-011435","doi":"https://doi.org/10.1146/annurev-biodatasci-102423-011435","is_oa":true,"landing_page_url":"https://doi.org/10.1146/annurev-biodatasci-102423-011435","pdf_url":null,"source":{"id":"https://openalex.org/S4210232080","display_name":"Annual Review of Biomedical Data Science","issn_l":"2574-3414","issn":["2574-3414"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","doyens","medline","norway-1","poland-20","russia-white-list-4"],"host_organization":"https://openalex.org/P4310320373","host_organization_name":"Annual Reviews","host_organization_lineage":["https://openalex.org/P4310320373"],"host_organization_lineage_names":["Annual Reviews"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Annual Review of Biomedical Data Science","raw_type":"journal-article"},{"id":"pmid:38603560","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38603560","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":"Annual review of biomedical data science","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:10704731","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11892350","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11892350/pdf/nihms-2061654.pdf","source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11892350","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11892350","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Annu Rev Biomed Data Sci","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1146/annurev-biodatasci-102423-011435","doi":"https://doi.org/10.1146/annurev-biodatasci-102423-011435","is_oa":true,"landing_page_url":"https://doi.org/10.1146/annurev-biodatasci-102423-011435","pdf_url":null,"source":{"id":"https://openalex.org/S4210232080","display_name":"Annual Review of Biomedical Data Science","issn_l":"2574-3414","issn":["2574-3414"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","doyens","medline","norway-1","poland-20","russia-white-list-4"],"host_organization":"https://openalex.org/P4310320373","host_organization_name":"Annual Reviews","host_organization_lineage":["https://openalex.org/P4310320373"],"host_organization_lineage_names":["Annual Reviews"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Annual Review of Biomedical Data Science","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1525192697","display_name":"Allosteric impact of non-active-site mutations on enzymatic function","funder_award_id":"R01GM124007","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6243465968","display_name":"Structural basis for ApoE4-induced Alzheimer's disease","funder_award_id":"RF1AG067194","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G9000890535","display_name":"Understanding and controlling protein energy landscapes by combining simulations and experiments","funder_award_id":"R35GM152085","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G9000899781","display_name":"Biology and pathobiology of apoE in aging and Alzheimer's disease","funder_award_id":"U19AG069701","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"}],"funders":[{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4394728357.pdf","grobid_xml":"https://content.openalex.org/works/W4394728357.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W2014050554","https://openalex.org/W2048822589","https://openalex.org/W2089879448","https://openalex.org/W2620864330","https://openalex.org/W2904865562","https://openalex.org/W2972246420","https://openalex.org/W3009690250","https://openalex.org/W3030773691","https://openalex.org/W3164917922","https://openalex.org/W3173575423","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3195375135","https://openalex.org/W3202105508","https://openalex.org/W3211795435","https://openalex.org/W4200268506","https://openalex.org/W4214847177","https://openalex.org/W4220745698","https://openalex.org/W4221071868","https://openalex.org/W4281551093","https://openalex.org/W4303614299","https://openalex.org/W4310058955","https://openalex.org/W4313880353","https://openalex.org/W4315927151","https://openalex.org/W4318220624","https://openalex.org/W4321117954","https://openalex.org/W4322732093","https://openalex.org/W4328102269","https://openalex.org/W4353031808","https://openalex.org/W4366290708","https://openalex.org/W4376226425","https://openalex.org/W4380576575","https://openalex.org/W4383903768","https://openalex.org/W4385664952","https://openalex.org/W4386861232","https://openalex.org/W4388829277","https://openalex.org/W4391389408","https://openalex.org/W4392843672","https://openalex.org/W4393249720","https://openalex.org/W4396895148"],"related_works":["https://openalex.org/W4382601731","https://openalex.org/W4408379310","https://openalex.org/W4407589131","https://openalex.org/W7116418940","https://openalex.org/W4407503584","https://openalex.org/W4415082342","https://openalex.org/W4406795926","https://openalex.org/W4415029131","https://openalex.org/W4407494284","https://openalex.org/W4407780908"],"abstract_inverted_index":{"Like":[0],"the":[1,5,35,71,83,119,135],"black":[2],"knight":[3],"in":[4,91,115],"classic":[6],"Monty":[7],"Python":[8],"movie,":[9],"grand":[10],"scientific":[11],"challenges":[12],"such":[13],"as":[14,62],"protein":[15,54,127,140,154,161],"folding":[16,55],"are":[17,98,113,151],"hard":[18],"to":[19,34,102,153,167],"finish":[20],"off.":[21],"Notably,":[22],"AlphaFold":[23],"is":[24,60,145,147],"revolutionizing":[25],"structural":[26],"biology":[27],"by":[28,137],"bringing":[29],"highly":[30],"accurate":[31],"structure":[32,50,103],"prediction":[33,104],"masses":[36],"and":[37,56,88,94,134,156,171],"opening":[38],"up":[39],"innumerable":[40],"new":[41,169],"avenues":[42],"of":[43,118,122,160],"research.":[44],"Despite":[45],"this":[46,142,158],"enormous":[47,120],"success,":[48],"calling":[49],"prediction,":[51],"much":[52],"less":[53],"related":[57],"problems,":[58],"\"solved\"":[59],"dangerous,":[61],"doing":[63],"so":[64],"could":[65],"stymie":[66],"further":[67,92],"progress.":[68],"Imagine":[69],"what":[70],"world":[72],"would":[73,107],"be":[74],"like":[75],"if":[76],"we":[77,106,112],"had":[78],"declared":[79],"flight":[80],"solved":[81],"after":[82],"first":[84],"commercial":[85],"airlines":[86],"opened":[87],"stopped":[89],"investing":[90],"research":[93],"development.":[95],"Likewise,":[96],"there":[97],"still":[99],"important":[100],"limitations":[101],"that":[105,148],"benefit":[108],"from":[109],"addressing.":[110],"Moreover,":[111],"limited":[114],"our":[116,165],"understanding":[117,157],"diversity":[121],"different":[123],"structures":[124],"a":[125,131,139],"single":[126],"can":[128],"adopt":[129],"(called":[130],"conformational":[132,149],"ensemble)":[133],"dynamics":[136,162],"which":[138],"explores":[141],"space.":[143],"What":[144],"clear":[146],"ensembles":[150],"critical":[152],"function,":[155],"aspect":[159],"will":[163],"advance":[164],"ability":[166],"design":[168],"proteins":[170],"drugs.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":20},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2024-04-12T00:00:00"}
