{"id":"https://openalex.org/W4387312302","doi":"https://doi.org/10.1021/acs.jcim.3c01387","title":"E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning","display_name":"E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning","publication_year":2023,"publication_date":"2023-10-03","ids":{"openalex":"https://openalex.org/W4387312302","doi":"https://doi.org/10.1021/acs.jcim.3c01387","pmid":"https://pubmed.ncbi.nlm.nih.gov/37788318"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01387","doi":"https://doi.org/10.1021/acs.jcim.3c01387","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01387","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2023/01/25/2023.01.25.525481.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101147265","display_name":"Haitao Zhu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hai-Tao Zhu","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109541284","display_name":"Yuhao Xia","orcid":"https://orcid.org/0009-0003-3323-5949","observed_orcids":["https://orcid.org/0009-0003-3323-5949"]},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu-Hao Xia","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049735973","display_name":"Guijun Zhang","orcid":"https://orcid.org/0000-0002-7815-5884","observed_orcids":["https://orcid.org/0000-0002-7815-5884"]},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Gui-Jun Zhang","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China"],"raw_orcid":"https://orcid.org/0000-0002-7815-5884","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China","institution_ids":["https://openalex.org/I55712492"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5049735973"],"corresponding_institution_ids":["https://openalex.org/I55712492"],"apc_list":{"value":5000,"currency":"USD","value_usd":5000},"apc_paid":null,"fwci":0.4533,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.49430102,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"63","issue":"20","first_page":"6451","last_page":"6461"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9926999807357788,"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":0.9926999807357788,"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":0.0026000000070780516,"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":0.002400000113993883,"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/multidomain-proteins","display_name":"multidomain proteins","score":0.8730000257492065},{"id":"https://openalex.org/keywords/rigid-body-motion","display_name":"rigid body motion","score":0.5770000219345093},{"id":"https://openalex.org/keywords/end-to-end-deep-learning","display_name":"end-to-end deep learning","score":0.6150000095367432},{"id":"https://openalex.org/keywords/efficientnetv2","display_name":"EfficientNetV2","score":0.8029999732971191},{"id":"https://openalex.org/keywords/attention-mechanism","display_name":"attention mechanism","score":0.9399999976158142},{"id":"https://openalex.org/keywords/model-scoring","display_name":"model scoring","score":0.3499999940395355},{"id":"https://openalex.org/keywords/gpu-memory-efficiency","display_name":"GPU memory efficiency","score":0.6930000185966492},{"id":"https://openalex.org/keywords/structure-based-drug-design","display_name":"structure-based drug design","score":0.7200000286102295}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7816489934921265},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.7162484526634216},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7115027904510498},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.597571849822998},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5450125932693481},{"id":"https://openalex.org/C74296488","wikidata":"https://www.wikidata.org/wiki/Q2527392","display_name":"End-to-end principle","level":2,"score":0.5138504505157471},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4823964834213257},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.42502039670944214},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38191449642181396},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3622286319732666},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33064889907836914},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32740408182144165},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1398138701915741},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.3c01387","doi":"https://doi.org/10.1021/acs.jcim.3c01387","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01387","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"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":"doi:10.1101/2023.01.25.525481","doi":"https://doi.org/10.1101/2023.01.25.525481","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1101/2023.01.25.525481","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2023/01/25/2023.01.25.525481.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:37788318","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37788318","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":"Journal of chemical information and modeling","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1101/2023.01.25.525481","doi":"https://doi.org/10.1101/2023.01.25.525481","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1101/2023.01.25.525481","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2023/01/25/2023.01.25.525481.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1320274221","display_name":null,"funder_award_id":"2022ZD0115103","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G285078680","display_name":null,"funder_award_id":"2022ZD0115100","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic of China"},{"id":"https://openalex.org/G320835743","display_name":null,"funder_award_id":"LZ20F030002","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3775454306","display_name":null,"funder_award_id":"62173304","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G460379816","display_name":null,"funder_award_id":"LZ20F030002","funder_id":"https://openalex.org/F4320338464","funder_display_name":"Natural Science Foundation of Zhejiang Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321540","display_name":"Ministry of Science and Technology of the People's Republic of China","ror":"https://ror.org/027s68j25"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320338464","display_name":"Natural Science Foundation of Zhejiang Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387312302.pdf","grobid_xml":"https://content.openalex.org/works/W4387312302.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W253094825","https://openalex.org/W1981264193","https://openalex.org/W2112792893","https://openalex.org/W2130479394","https://openalex.org/W2130581715","https://openalex.org/W2144112190","https://openalex.org/W2147805410","https://openalex.org/W2151581834","https://openalex.org/W2152517415","https://openalex.org/W2156628505","https://openalex.org/W2166701319","https://openalex.org/W2170449429","https://openalex.org/W2170471837","https://openalex.org/W2170747616","https://openalex.org/W2179537696","https://openalex.org/W2406171343","https://openalex.org/W2557595285","https://openalex.org/W2559007573","https://openalex.org/W2620998958","https://openalex.org/W2960589734","https://openalex.org/W2963436022","https://openalex.org/W2971003495","https://openalex.org/W2972411752","https://openalex.org/W2980272550","https://openalex.org/W2987090428","https://openalex.org/W2997234557","https://openalex.org/W2999044305","https://openalex.org/W3037620288","https://openalex.org/W3040739508","https://openalex.org/W3121000782","https://openalex.org/W3146944767","https://openalex.org/W3165545667","https://openalex.org/W3173197060","https://openalex.org/W3175798418","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3178212622","https://openalex.org/W3186179742","https://openalex.org/W3209492740","https://openalex.org/W3211795435","https://openalex.org/W3212854871","https://openalex.org/W4205827692","https://openalex.org/W4211238482","https://openalex.org/W4291237297","https://openalex.org/W4300861364","https://openalex.org/W4306711252","https://openalex.org/W4309452766","https://openalex.org/W4310951880","https://openalex.org/W4323075934","https://openalex.org/W4327550249","https://openalex.org/W4386065518"],"related_works":["https://openalex.org/W4324311504","https://openalex.org/W4291237297","https://openalex.org/W4410078871","https://openalex.org/W4226302535","https://openalex.org/W4295165394","https://openalex.org/W7163882486","https://openalex.org/W4375856720","https://openalex.org/W4389235501","https://openalex.org/W4410621619","https://openalex.org/W4409201509"],"abstract_inverted_index":{"Abstract":[0],"With":[1],"the":[2,18,35,38,48,61,66,78,81,87,102,110,169,200,216,220,226,257,266,283,286,292,299,307],"development":[3],"of":[4,21,37,68,183,219,285,296],"deep":[5,127,136],"learning,":[6,128],"almost":[7],"all":[8],"single-domain":[9,82,166],"proteins":[10,23,185],"can":[11,73,107,275,317],"be":[12,74],"predicted":[13,85,170,269,288],"at":[14,329],"experimental":[15,212],"resolution.":[16],"However,":[17],"structure":[19,83],"prediction":[20,89],"multi-domain":[22,184],"remains":[24],"a":[25,69,98,192],"challenge.":[26],"Achieving":[27],"end-to-end":[28,324],"protein":[29,71,252],"domain":[30,103,237,308],"assembly":[31,49,104,209,238,309,320],"and":[32,94,165,244],"further":[33],"improving":[34,47],"accuracy":[36],"full-chain":[39,70,99,181,267],"modelling":[40],"by":[41,86,158,223,260,270,289,303],"accurately":[42],"predicting":[43,144],"inter-domain":[44,145,155,176,279],"orientation":[45],"while":[46],"efficiency":[50,321],"will":[51],"provide":[52],"significant":[53],"insights":[54],"into":[55,97,175],"structure-based":[56],"drug":[57],"discovery.":[58],"In":[59,115],"addition,":[60],"available":[62],"GPU":[63],"memory":[64],"limits":[65],"size":[67],"which":[72,106,140,232,313],"predicted.":[75],"Based":[76],"on":[77,126,225,248,298],"divide-and-conquer":[79],"strategy,":[80,194],"is":[84,141,196,230,233,262,301,328],"state-of-the-art":[88],"method,":[90,105],"such":[91],"as":[92],"AlphaFold2,":[93,271],"then":[95],"assembled":[96,205,222],"model":[100,138,202,221,258,268,287],"through":[101,322],"effectively":[108,318],"reduce":[109],"demand":[111],"for":[112,143],"hardware":[113],"resources.":[114],"this":[116],"work,":[117],"we":[118],"propose":[119],"an":[120,134,150,323],"End-To-End":[121],"Domain":[122],"Assembly":[123],"method":[124,311],"based":[125],"named":[129],"E2EDA.":[130],"We":[131],"first":[132],"develop":[133],"EffificientNetV2-based":[135],"learning":[137],"(RMNet),":[139],"specialised":[142],"orientations.":[146],"The":[147,211],"RMNet":[148],"uses":[149],"attention":[151],"mechanism":[152],"to":[153,179,198,207,281],"predict":[154],"rigid":[156,171],"motion":[157],"fusing":[159],"sequence":[160],"features,":[161],"multiple":[162,204],"template":[163],"features":[164],"features.":[167],"Then,":[168],"motions":[172],"are":[173],"converted":[174],"spatial":[177],"transformations":[178],"assemble":[180],"models":[182,206],"directly":[186],"without":[187],"time-consuming":[188],"simulation":[189,310],"processes.":[190],"Finally,":[191],"scoring":[193],"RMscore,":[195],"designed":[197],"select":[199],"best":[201],"from":[203,254],"improve":[208,282,319],"accuracy.":[210],"results":[213],"show":[214],"that":[215,273,315],"average":[217,293],"TM-score":[218],"E2EDA":[224,261,274,297,316],"benchmark":[227,300],"set":[228],"(356)":[229],"0.84,":[231],"better":[234],"than":[235,265],"other":[236],"methods":[239],"SADA":[240],"(0.80),":[241],"DEMO":[242],"(0.74)":[243],"AIDA":[245],"(0.63).":[246],"Meanwhile,":[247],"our":[249],"constructed":[250],"human":[251],"dataset":[253],"AlphaFold":[255],"DB,":[256],"reassembled":[259],"6.8%":[263],"higher":[264],"indicating":[272],"capture":[276],"more":[277],"accurate":[278],"orientations":[280],"quality":[284],"AlphaFold2.":[290],"Furthermore,":[291],"running":[294],"time":[295],"reduced":[302],"74.6%":[304],"compared":[305],"with":[306],"SADA,":[312],"indicates":[314],"manner.The":[325],"online":[326],"server":[327],"http://zhanglab-bioinf.com/E2EDA/":[330],".":[331]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2023-10-04T00:00:00"}