{"id":"https://openalex.org/W3027554922","doi":"https://doi.org/10.1093/bioinformatics/btaa531","title":"SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction","display_name":"SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction","publication_year":2020,"publication_date":"2020-05-16","ids":{"openalex":"https://openalex.org/W3027554922","doi":"https://doi.org/10.1093/bioinformatics/btaa531","mag":"3027554922","pmid":"https://pubmed.ncbi.nlm.nih.gov/32437517"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa531","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa531","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108936928","display_name":"Mostofa Rafid Uddin","orcid":null},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]},{"id":"https://openalex.org/I885507782","display_name":"East West University","ror":"https://ror.org/05p0tzt32","country_code":"BD","type":"education","lineage":["https://openalex.org/I885507782"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Mostofa Rafid Uddin","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","Department of Computer Science and Engineering, East West University , Dhaka 1212, Bangladesh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, East West University , Dhaka 1212, Bangladesh","institution_ids":["https://openalex.org/I885507782"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081666457","display_name":"Sazan Mahbub","orcid":"https://orcid.org/0000-0002-8667-3649"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Sazan Mahbub","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100733249","display_name":"Mohammad Saifur Rahman","orcid":"https://orcid.org/0000-0002-9887-4456"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"M Saifur Rahman","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"],"raw_orcid":"https://orcid.org/0000-0002-9887-4456","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063693993","display_name":"Md. Shamsuzzoha Bayzid","orcid":"https://orcid.org/0000-0002-5640-0615"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":true,"raw_author_name":"Md Shamsuzzoha Bayzid","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"],"raw_orcid":"https://orcid.org/0000-0002-5640-0615","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5063693993"],"corresponding_institution_ids":["https://openalex.org/I183697816"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.4752,"has_fulltext":false,"cited_by_count":78,"citation_normalized_percentile":{"value":0.95809831,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"36","issue":"17","first_page":"4599","last_page":"4608"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7548999786376953,"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":0.7548999786376953,"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":0.16259999573230743,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.02419999986886978,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8272100687026978},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7246006727218628},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.551421582698822},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5242170095443726},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5045844316482544},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.4179021418094635},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4019823670387268}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8272100687026978},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7246006727218628},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.551421582698822},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5242170095443726},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5045844316482544},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.4179021418094635},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4019823670387268},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa531","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa531","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32437517","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32437517","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,"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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F261270187","display_name":"Information and Communication Technology Division","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":107,"referenced_works":["https://openalex.org/W1490308602","https://openalex.org/W1583837637","https://openalex.org/W1601251682","https://openalex.org/W1689711448","https://openalex.org/W1758266623","https://openalex.org/W1902237438","https://openalex.org/W1930795817","https://openalex.org/W1979826517","https://openalex.org/W1985818354","https://openalex.org/W1987328021","https://openalex.org/W2002272439","https://openalex.org/W2004461664","https://openalex.org/W2004733253","https://openalex.org/W2008708467","https://openalex.org/W2045716015","https://openalex.org/W2045777307","https://openalex.org/W2051210555","https://openalex.org/W2057157558","https://openalex.org/W2059136964","https://openalex.org/W2064675550","https://openalex.org/W2072404760","https://openalex.org/W2078535469","https://openalex.org/W2093989924","https://openalex.org/W2097606916","https://openalex.org/W2100890997","https://openalex.org/W2104972430","https://openalex.org/W2106693479","https://openalex.org/W2107878631","https://openalex.org/W2119423166","https://openalex.org/W2122945697","https://openalex.org/W2128801478","https://openalex.org/W2129020329","https://openalex.org/W2130479394","https://openalex.org/W2131474431","https://openalex.org/W2131801377","https://openalex.org/W2133564696","https://openalex.org/W2134299061","https://openalex.org/W2140992384","https://openalex.org/W2144578941","https://openalex.org/W2147209844","https://openalex.org/W2150987569","https://openalex.org/W2153153865","https://openalex.org/W2153187042","https://openalex.org/W2156798505","https://openalex.org/W2157437977","https://openalex.org/W2158714788","https://openalex.org/W2161062388","https://openalex.org/W2170471837","https://openalex.org/W2267186426","https://openalex.org/W2402302915","https://openalex.org/W2413794162","https://openalex.org/W2417356443","https://openalex.org/W2559655401","https://openalex.org/W2562607067","https://openalex.org/W2566370974","https://openalex.org/W2567587907","https://openalex.org/W2606974598","https://openalex.org/W2607268717","https://openalex.org/W2612690371","https://openalex.org/W2739202500","https://openalex.org/W2757154661","https://openalex.org/W2781528640","https://openalex.org/W2791790018","https://openalex.org/W2802048770","https://openalex.org/W2804078698","https://openalex.org/W2808950571","https://openalex.org/W2809216727","https://openalex.org/W2887428522","https://openalex.org/W2888258099","https://openalex.org/W2900952222","https://openalex.org/W2905446269","https://openalex.org/W2913201579","https://openalex.org/W2924700250","https://openalex.org/W2943717199","https://openalex.org/W2945034620","https://openalex.org/W2945214237","https://openalex.org/W2950197776","https://openalex.org/W2950374603","https://openalex.org/W2950527759","https://openalex.org/W2951092885","https://openalex.org/W2962965405","https://openalex.org/W2963271116","https://openalex.org/W2963374347","https://openalex.org/W2963457143","https://openalex.org/W2964199361","https://openalex.org/W2964308564","https://openalex.org/W2973280817","https://openalex.org/W3097079079","https://openalex.org/W3127111995","https://openalex.org/W4211054902","https://openalex.org/W4236965008","https://openalex.org/W4297796913","https://openalex.org/W4301409532","https://openalex.org/W4303633609","https://openalex.org/W4394665226","https://openalex.org/W6639478124","https://openalex.org/W6679434410","https://openalex.org/W6684821475","https://openalex.org/W6684941089","https://openalex.org/W6712909570","https://openalex.org/W6726186668","https://openalex.org/W6731867162","https://openalex.org/W6734247333","https://openalex.org/W6752378368","https://openalex.org/W6756396466","https://openalex.org/W6762658016","https://openalex.org/W6864315806"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W4246352526","https://openalex.org/W2121910908","https://openalex.org/W915438175","https://openalex.org/W4230315250"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein":[1],"structures":[2],"provide":[3],"basic":[4],"insight":[5],"into":[6],"how":[7],"they":[8],"can":[9],"interact":[10],"with":[11,119,167],"other":[12],"proteins,":[13],"their":[14],"functions":[15],"and":[16,27,43,88,132,182,194,208,226],"biological":[17],"roles":[18],"in":[19,62,124,165],"an":[20,155,241],"organism.":[21],"Experimental":[22],"methods":[23,68,171],"(e.g.":[24],"X-ray":[25],"crystallography":[26],"nuclear":[28],"magnetic":[29],"resonance":[30],"spectroscopy)":[31],"for":[32,51,105],"predicting":[33,52],"the":[34,53,94,120,130,136,147,161,168,191,196,203,210,224],"secondary":[35],"structure":[36,76,107],"(SS)":[37],"of":[38,55,58,82,163,175,205,229,231],"proteins":[39],"are":[40],"very":[41],"expensive":[42],"time":[44],"consuming.":[45],"Therefore,":[46],"developing":[47,63],"efficient":[48],"computational":[49],"approaches":[50],"SS":[54,66,83],"protein":[56],"is":[57,89,202,237],"utmost":[59],"importance.":[60],"Advances":[61],"highly":[64,102],"accurate":[65,103,225],"prediction":[67,192,228],"have":[69],"mostly":[70],"been":[71],"focused":[72],"on":[73,172],"3-class":[74],"(Q3)":[75],"prediction.":[77,96],"However,":[78],"8-class":[79],"(Q8)":[80],"resolution":[81],"contains":[84],"more":[85,91,143],"useful":[86],"information":[87],"much":[90],"challenging":[92],"than":[93,146],"Q3":[95],"RESULTS:":[97],"We":[98],"present":[99],"SAINT,":[100],"a":[101,142,173,220],"method":[104],"Q8":[106,213],"prediction,":[108],"which":[109],"incorporates":[110],"self-attention":[111,188],"mechanism":[112,189],"(a":[113],"concept":[114],"from":[115],"natural":[116],"language":[117],"processing)":[118],"Deep":[121],"Inception-Inside-Inception":[122],"network":[123,152],"order":[125],"to":[126],"effectively":[127],"capture":[128],"both":[129],"short-":[131],"long-range":[133],"interactions":[134],"among":[135],"amino":[137],"acid":[138],"residues.":[139],"SAINT":[140,164,201,218,236],"offers":[141,209],"interpretable":[144],"framework":[145],"typical":[148],"black-box":[149],"deep":[150],"neural":[151],"methods.":[153,200],"Through":[154],"extensive":[156],"evaluation":[157],"study,":[158],"we":[159,216],"report":[160],"performance":[162],"comparison":[166],"existing":[169,197],"best":[170,198,211],"collection":[174],"benchmark":[176],"datasets,":[177],"namely,":[178],"TEST2016,":[179],"TEST2018,":[180],"CASP12":[181],"CASP13.":[183],"Our":[184],"results":[185],"suggest":[186],"that":[187],"improves":[190],"accuracy":[193],"outperforms":[195],"alternate":[199],"first":[204],"its":[206],"kind":[207],"known":[212],"accuracy.":[214],"Thus,":[215],"believe":[217],"represents":[219],"major":[221],"step":[222],"toward":[223],"reliable":[227],"SSs":[230],"proteins.":[232],"AVAILABILITY":[233],"AND":[234],"IMPLEMENTATION:":[235],"freely":[238],"available":[239],"as":[240],"open-source":[242],"project":[243],"at":[244],"https://github.com/SAINTProtein/SAINT.":[245]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}