{"id":"https://openalex.org/W3201869122","doi":"https://doi.org/10.1021/acs.jcim.1c01114","title":"AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function","display_name":"AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function","publication_year":2021,"publication_date":"2021-09-29","ids":{"openalex":"https://openalex.org/W3201869122","doi":"https://doi.org/10.1021/acs.jcim.1c01114","mag":"3201869122"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c01114","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01114","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8592092","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010808261","display_name":"Jeffrey Skolnick","orcid":"https://orcid.org/0000-0002-1877-4958"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeffrey Skolnick","raw_affiliation_strings":["Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States"],"affiliations":[{"raw_affiliation_string":"Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000947559","display_name":"Mu Gao","orcid":"https://orcid.org/0000-0002-0378-3704"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mu Gao","raw_affiliation_strings":["Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States"],"affiliations":[{"raw_affiliation_string":"Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022257357","display_name":"Hongyi Zhou","orcid":"https://orcid.org/0000-0001-5074-5180"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongyi Zhou","raw_affiliation_strings":["Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States"],"affiliations":[{"raw_affiliation_string":"Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069974203","display_name":"Suresh B. Singh","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Suresh Singh","raw_affiliation_strings":["Twilight Design, 4 Adams Road, Kendall Park, New Jersey 08824, United States"],"affiliations":[{"raw_affiliation_string":"Twilight Design, 4 Adams Road, Kendall Park, New Jersey 08824, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5010808261"],"corresponding_institution_ids":["https://openalex.org/I130701444"],"apc_list":null,"apc_paid":null,"fwci":14.1493,"has_fulltext":false,"cited_by_count":252,"citation_normalized_percentile":{"value":0.99481295,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"61","issue":"10","first_page":"4827","last_page":"4831"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9987000226974487,"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":0.9987000226974487,"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":0.9925000071525574,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9828000068664551,"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/computer-science","display_name":"Computer science","score":0.6185718774795532},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5885365009307861},{"id":"https://openalex.org/keywords/completeness","display_name":"Completeness (order theory)","score":0.5873977541923523},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5335261225700378},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5249502658843994},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4782108962535858},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.45141980051994324},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.4417736530303955},{"id":"https://openalex.org/keywords/resolution","display_name":"Resolution (logic)","score":0.4355854392051697},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.42657166719436646},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41411399841308594},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36828169226646423},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2728973627090454},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1762966513633728},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15314391255378723}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6185718774795532},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5885365009307861},{"id":"https://openalex.org/C17231256","wikidata":"https://www.wikidata.org/wiki/Q5156540","display_name":"Completeness (order theory)","level":2,"score":0.5873977541923523},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5335261225700378},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5249502658843994},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4782108962535858},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.45141980051994324},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.4417736530303955},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.4355854392051697},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.42657166719436646},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41411399841308594},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36828169226646423},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2728973627090454},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1762966513633728},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15314391255378723},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c01114","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01114","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8592092","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8592092","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8592092","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8592092","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7185028031","display_name":null,"funder_award_id":"GM-118039","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W1600959429","https://openalex.org/W1969327849","https://openalex.org/W1982583124","https://openalex.org/W1998173128","https://openalex.org/W2010931041","https://openalex.org/W2011495938","https://openalex.org/W2031368570","https://openalex.org/W2037312364","https://openalex.org/W2038117444","https://openalex.org/W2051268589","https://openalex.org/W2053260890","https://openalex.org/W2059517336","https://openalex.org/W2067852761","https://openalex.org/W2070888644","https://openalex.org/W2081208252","https://openalex.org/W2093769098","https://openalex.org/W2099254366","https://openalex.org/W2102245393","https://openalex.org/W2116836989","https://openalex.org/W2117340986","https://openalex.org/W2121125726","https://openalex.org/W2121911824","https://openalex.org/W2126679079","https://openalex.org/W2139774535","https://openalex.org/W2144258433","https://openalex.org/W2146190809","https://openalex.org/W2155201844","https://openalex.org/W2160902835","https://openalex.org/W2166912610","https://openalex.org/W2171641243","https://openalex.org/W2219859606","https://openalex.org/W2416913394","https://openalex.org/W2611792444","https://openalex.org/W2804171113","https://openalex.org/W2809303314","https://openalex.org/W2894906875","https://openalex.org/W2918296775","https://openalex.org/W2922340164","https://openalex.org/W2944535254","https://openalex.org/W2967606876","https://openalex.org/W2997234557","https://openalex.org/W2999044305","https://openalex.org/W3014239097","https://openalex.org/W3056303605","https://openalex.org/W3078690673","https://openalex.org/W3088634596","https://openalex.org/W3088911218","https://openalex.org/W3089408272","https://openalex.org/W3094695530","https://openalex.org/W3114734220","https://openalex.org/W3124030253","https://openalex.org/W3128355392","https://openalex.org/W3136158255","https://openalex.org/W3161758072","https://openalex.org/W3163965514","https://openalex.org/W3164059188","https://openalex.org/W3177828909","https://openalex.org/W3183475563","https://openalex.org/W3185358186","https://openalex.org/W3186179742","https://openalex.org/W3186340132","https://openalex.org/W4246356731"],"related_works":["https://openalex.org/W2806488847","https://openalex.org/W4353055924","https://openalex.org/W2732388178","https://openalex.org/W4361279638","https://openalex.org/W2121688928","https://openalex.org/W4401895022","https://openalex.org/W3126783617","https://openalex.org/W3093468851","https://openalex.org/W4405545553","https://openalex.org/W4387012733"],"abstract_inverted_index":{"AlphaFold":[0],"2":[1],"(AF2)":[2],"was":[3],"the":[4,8,20,54,57,91],"star":[5],"of":[6,22,37,56,59,86,93],"CASP14,":[7],"last":[9],"biannual":[10],"structure":[11],"prediction":[12],"experiment.":[13],"Using":[14],"novel":[15],"deep":[16],"learning,":[17],"AF2":[18,39],"predicted":[19],"structures":[21,92],"many":[23,94],"difficult":[24],"protein":[25],"targets":[26],"at":[27,97],"or":[28,98],"near":[29],"experimental":[30],"resolution.":[31,81],"Here,":[32],"we":[33],"present":[34],"our":[35],"perspective":[36],"why":[38],"works":[40],"and":[41,84],"show":[42],"that":[43,52,73],"it":[44,75],"is":[45],"a":[46],"very":[47],"sophisticated":[48],"fold":[49],"recognition":[50],"algorithm":[51],"exploits":[53],"completeness":[55],"library":[58],"single":[60],"domain":[61],"PDB":[62],"structures.":[63],"It":[64],"has":[65],"also":[66],"learned":[67],"local":[68],"side":[69],"chain":[70],"packing":[71],"rearrangements":[72],"enable":[74],"to":[76,79,89,100],"refine":[77],"proteins":[78,96],"high":[80],"The":[82],"benefits":[83],"limitations":[85],"its":[87],"ability":[88],"predict":[90],"more":[95],"close":[99],"atomic":[101],"detail":[102],"are":[103],"discussed.":[104]},"counts_by_year":[{"year":2026,"cited_by_count":15},{"year":2025,"cited_by_count":61},{"year":2024,"cited_by_count":68},{"year":2023,"cited_by_count":71},{"year":2022,"cited_by_count":33},{"year":2021,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2021-10-11T00:00:00"}