{"id":"https://openalex.org/W3042567394","doi":"https://doi.org/10.1093/bioinformatics/btaa629","title":"OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks","display_name":"OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks","publication_year":2020,"publication_date":"2020-07-10","ids":{"openalex":"https://openalex.org/W3042567394","doi":"https://doi.org/10.1093/bioinformatics/btaa629","mag":"3042567394","pmid":"https://pubmed.ncbi.nlm.nih.gov/32678893"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa629","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa629","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/20/5021/35065215/btaa629.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/20/5021/35065215/btaa629.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049642190","display_name":"Gang Xu","orcid":"https://orcid.org/0000-0003-0616-878X"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gang Xu","raw_affiliation_strings":["Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100432288","display_name":"Qinghua Wang","orcid":"https://orcid.org/0000-0002-0480-3404"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qinghua Wang","raw_affiliation_strings":["Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076174923","display_name":"Jianpeng Ma","orcid":"https://orcid.org/0000-0003-2943-0779"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Jianpeng Ma","raw_affiliation_strings":["Department of Bioengineering, Rice University , Houston, TX 77030, USA","Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433, China","Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Rice University , Houston, TX 77030, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I181547552"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5076174923"],"corresponding_institution_ids":["https://openalex.org/I181547552","https://openalex.org/I24943067","https://openalex.org/I74775410"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.6615,"has_fulltext":false,"cited_by_count":61,"citation_normalized_percentile":{"value":0.94322551,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"36","issue":"20","first_page":"5021","last_page":"5026"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8812000155448914,"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":0.8812000155448914,"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":0.0632999986410141,"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":0.013299999758601189,"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/opus","display_name":"Opus","score":0.6943044662475586},{"id":"https://openalex.org/keywords/casp","display_name":"CASP","score":0.6350215673446655},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.5628528594970703},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5362585783004761},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5308371782302856},{"id":"https://openalex.org/keywords/torsion","display_name":"Torsion (gastropod)","score":0.5288577675819397},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.44341424107551575},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.44087499380111694},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.41957688331604004},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3548790216445923},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3258506655693054},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.2778790593147278},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.15414667129516602},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09499001502990723}],"concepts":[{"id":"https://openalex.org/C2778950570","wikidata":"https://www.wikidata.org/wiki/Q1466199","display_name":"Opus","level":2,"score":0.6943044662475586},{"id":"https://openalex.org/C66153294","wikidata":"https://www.wikidata.org/wiki/Q899291","display_name":"CASP","level":4,"score":0.6350215673446655},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5628528594970703},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5362585783004761},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5308371782302856},{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.5288577675819397},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.44341424107551575},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44087499380111694},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.41957688331604004},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3548790216445923},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3258506655693054},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.2778790593147278},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.15414667129516602},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09499001502990723},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa629","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa629","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/20/5021/35065215/btaa629.pdf","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:32678893","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32678893","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":{"id":"doi:10.1093/bioinformatics/btaa629","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa629","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/20/5021/35065215/btaa629.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4771822614","display_name":null,"funder_award_id":"2019YFC1711600","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6948812679","display_name":null,"funder_award_id":"Q-1512","funder_id":"https://openalex.org/F4320306196","funder_display_name":"Welch Foundation"},{"id":"https://openalex.org/G8327369822","display_name":null,"funder_award_id":"Q-1826","funder_id":"https://openalex.org/F4320306196","funder_display_name":"Welch Foundation"}],"funders":[{"id":"https://openalex.org/F4320306196","display_name":"Welch Foundation","ror":"https://ror.org/00np6vq88"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1596947964","https://openalex.org/W2008708467","https://openalex.org/W2030990710","https://openalex.org/W2051210555","https://openalex.org/W2057289558","https://openalex.org/W2064675550","https://openalex.org/W2088608587","https://openalex.org/W2094458603","https://openalex.org/W2095705004","https://openalex.org/W2102461176","https://openalex.org/W2107024517","https://openalex.org/W2112796928","https://openalex.org/W2115167726","https://openalex.org/W2118387386","https://openalex.org/W2126103104","https://openalex.org/W2131774270","https://openalex.org/W2145268834","https://openalex.org/W2153153865","https://openalex.org/W2158714788","https://openalex.org/W2342838938","https://openalex.org/W2557595285","https://openalex.org/W2607268717","https://openalex.org/W2626778328","https://openalex.org/W2753650356","https://openalex.org/W2791790018","https://openalex.org/W2802316666","https://openalex.org/W2804822363","https://openalex.org/W2808950571","https://openalex.org/W2905446269","https://openalex.org/W2919115771","https://openalex.org/W2950374603","https://openalex.org/W2950865779","https://openalex.org/W2951433247","https://openalex.org/W2951599627","https://openalex.org/W2951639995","https://openalex.org/W2952317511","https://openalex.org/W2967606876","https://openalex.org/W2969644707","https://openalex.org/W2971733377","https://openalex.org/W2972411752","https://openalex.org/W2999044305","https://openalex.org/W2999989051","https://openalex.org/W3018227322","https://openalex.org/W3027554922","https://openalex.org/W4211196614","https://openalex.org/W4255594044","https://openalex.org/W4385245566","https://openalex.org/W6674330103","https://openalex.org/W6739901393","https://openalex.org/W6763868836","https://openalex.org/W6767992085"],"related_works":["https://openalex.org/W2928838901","https://openalex.org/W2946599741","https://openalex.org/W1966040491","https://openalex.org/W2147472674","https://openalex.org/W4225106352","https://openalex.org/W1888349473","https://openalex.org/W2997512804","https://openalex.org/W4287907454","https://openalex.org/W1567853508","https://openalex.org/W2471429531"],"abstract_inverted_index":{"MOTIVATION:":[0],"Predictions":[1],"of":[2,25,79,86,106,127,200,292],"protein":[3,19],"backbone":[4,184],"torsion":[5,185,254],"angles":[6,186,255],"(\u03d5":[7],"and":[8,10,55,108,118,129,135,150,159,188,202,206,210,215,222,230,234,237,239,243,272,280,288,294],"\u03c8)":[9],"secondary":[11,189,217,245],"structure":[12,20,164,190,218,246],"from":[13,166],"sequence":[14],"are":[15,220,275,297,305],"crucial":[16],"subproblems":[17],"in":[18,140,155,182],"prediction.":[21,191],"With":[22],"the":[23,37,65,68,84,94,115,125,141,156,196,211,260,265,289],"development":[24],"deep":[26],"learning":[27,81],"approaches,":[28],"their":[29,48],"accuracies":[30,212],"have":[31],"been":[32],"significantly":[33],"improved.":[34],"To":[35],"capture":[36,64],"long-range":[38],"interactions,":[39],"most":[40],"studies":[41],"integrate":[42],"bidirectional":[43],"recurrent":[44],"neural":[45,87],"networks":[46],"into":[47,93],"models.":[49],"In":[50,225,249],"this":[51],"study,":[52],"we":[53,76],"introduce":[54],"modify":[56],"a":[57,160],"recently":[58,161],"proposed":[59,139,154],"architecture":[60],"named":[61,170],"Transformer":[62],"to":[63,82,98,278],"interactions":[66],"between":[67],"two":[69],"residues":[70],"theoretically":[71],"with":[72],"arbitrary":[73],"distance.":[74],"Moreover,":[75],"take":[77],"advantage":[78],"multitask":[80],"improve":[83],"generalization":[85],"network":[88],"by":[89],"introducing":[90],"related":[91],"tasks":[92],"training":[95,117,287],"process.":[96],"Similar":[97],"many":[99],"previous":[100],"studies,":[101],"OPUS-TASS":[102,113,128,178,227,293],"uses":[103,114],"an":[104],"ensemble":[105],"models":[107],"achieves":[109,179,195,228],"better":[110],"results.":[111],"RESULTS:":[112],"same":[116],"validation":[119],"sets":[120],"as":[121,171,259],"SPOT-1D.":[122],"We":[123],"compare":[124],"performance":[126],"SPOT-1D":[130,142,194],"on":[131],"TEST2016":[132],"(1213":[133],"proteins)":[134,138,149,153,169],"TEST2018":[136],"(250":[137],"paper,":[143,158],"CASP12":[144],"(55":[145],"proteins),":[146],"CASP13":[147],"(32":[148],"CASP-FM":[151],"(56":[152],"SAINT":[157],"released":[162],"PDB":[163],"collection":[165],"CAMEO":[167],"(93":[168],"CAMEO93.":[172],"On":[173,192],"these":[174],"six":[175],"test":[176],"sets,":[177],"consistent":[180],"improvements":[181],"both":[183],"prediction":[187],"CAMEO93,":[193],"mean":[197,266],"absolute":[198,267],"errors":[199,268],"16.89":[201],"23.02":[203],"for":[204,213,232,241,263,269],"\u03d5":[205,233,271],"\u03c8":[207,235,273],"predictions,":[208,236,247],"respectively,":[209],"3-":[214,242],"8-state":[216,244],"predictions":[219,274],"87.72":[221],"77.15%,":[223],"respectively.":[224,248,282],"comparison,":[226],"16.56":[229],"22.56":[231],"89.06":[238],"78.87%":[240],"particular,":[250],"after":[251],"using":[252],"our":[253],"refinement":[256],"method":[257],"OPUS-Refine":[258],"post-processing":[261],"procedure":[262],"OPUS-TASS,":[264],"final":[270],"further":[276],"decreased":[277],"16.28":[279],"21.98,":[281],"AVAILABILITY":[283],"AND":[284],"IMPLEMENTATION:":[285],"The":[286],"inference":[290],"codes":[291],"its":[295],"data":[296,304],"available":[298,306],"at":[299,307],"https://github.com/thuxugang/opus_tass.":[300],"SUPPLEMENTARY":[301],"INFORMATION:":[302],"Supplementary":[303],"Bioinformatics":[308],"online.":[309]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}