{"id":"https://openalex.org/W4405427338","doi":"https://doi.org/10.1145/3698587.3701400","title":"AttCON-Homo: Attention and PLMs-enhanced Neural Networks for Predicting Inter-chain Contacts and Distances in Homo-oligomeric Protein Complexes","display_name":"AttCON-Homo: Attention and PLMs-enhanced Neural Networks for Predicting Inter-chain Contacts and Distances in Homo-oligomeric Protein Complexes","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4405427338","doi":"https://doi.org/10.1145/3698587.3701400"},"language":"en","primary_location":{"id":"doi:10.1145/3698587.3701400","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3698587.3701400","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5112967678","display_name":"Che Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Che Zhao","raw_affiliation_strings":["School of Information Science and Engineering, Yunnan University, Kunming, Yunnan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Yunnan University, Kunming, Yunnan, China","institution_ids":["https://openalex.org/I189210763"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040105964","display_name":"Shunfang Wang","orcid":"https://orcid.org/0000-0002-1927-8753"},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shunfang Wang","raw_affiliation_strings":["School of Information Science and Engineering, Yunnan University, Kunming, Yunnan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Yunnan University, Kunming, Yunnan, China","institution_ids":["https://openalex.org/I189210763"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5112967678"],"corresponding_institution_ids":["https://openalex.org/I189210763"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.20295567,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.996399998664856,"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":0.996399998664856,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9914000034332275,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9635999798774719,"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/artificial-neural-network","display_name":"Artificial neural network","score":0.5649316906929016},{"id":"https://openalex.org/keywords/chain","display_name":"Chain (unit)","score":0.4740145802497864},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43237045407295227},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3724813461303711},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.17161324620246887}],"concepts":[{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5649316906929016},{"id":"https://openalex.org/C199185054","wikidata":"https://www.wikidata.org/wiki/Q552299","display_name":"Chain (unit)","level":2,"score":0.4740145802497864},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43237045407295227},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3724813461303711},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.17161324620246887},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3698587.3701400","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3698587.3701400","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1915291795","display_name":null,"funder_award_id":"62462068,62062067","funder_id":"https://openalex.org/F4320323817","funder_display_name":"Universitas Brawijaya"}],"funders":[{"id":"https://openalex.org/F4320323817","display_name":"Universitas Brawijaya","ror":"https://ror.org/01wk3d929"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W2051210555","https://openalex.org/W2102461176","https://openalex.org/W2152495216","https://openalex.org/W2557595285","https://openalex.org/W2884585870","https://openalex.org/W2949342052","https://openalex.org/W2950954328","https://openalex.org/W2953008890","https://openalex.org/W2998508940","https://openalex.org/W3034552520","https://openalex.org/W3106340289","https://openalex.org/W3133458480","https://openalex.org/W3133540795","https://openalex.org/W3177828909","https://openalex.org/W3193795503","https://openalex.org/W3211403530","https://openalex.org/W3212532687","https://openalex.org/W4210646117","https://openalex.org/W4309190357","https://openalex.org/W4327550249","https://openalex.org/W4361228745","https://openalex.org/W4387772748","https://openalex.org/W4389329103","https://openalex.org/W6696761078"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Protein-protein":[0],"contacts":[1,18,136,156],"or":[2,19],"distances":[3,20],"prediction":[4,54,125],"is":[5,22],"crucial":[6],"for":[7],"the":[8,11,27,141,150],"modeling":[9],"of":[10,14,29,66,73,140,153,161],"quaternary":[12],"structure":[13],"protein":[15,32,68,81],"complexes,":[16],"this":[17],"information":[21],"also":[23],"widely":[24],"applied":[25],"in":[26,123,143],"development":[28],"drugs":[30],"and":[31,63,86,121,133],"function":[33],"prediction.":[34],"Currently,":[35],"many":[36],"methods":[37],"focus":[38],"on":[39,59,111],"predicting":[40,60],"inter-chain":[41,135],"contacts,":[42],"but":[43],"achieving":[44],"precise":[45],"predictions":[46],"remains":[47],"challenging.":[48],"Here,":[49],"we":[50],"have":[51],"developed":[52],"a":[53],"model,":[55],"AttCON-Homo,":[56],"which":[57],"focuses":[58],"both":[61],"contact":[62],"distance":[64],"maps":[65,77],"homo-oligomeric":[67],"complexes.":[69],"The":[70],"input":[71],"features":[72,89],"AttCON-Homo":[74,96,114,158],"integrate":[75],"attention":[76,99],"generated":[78],"by":[79,157],"two":[80],"language":[82],"models":[83],"(PLMs),":[84],"ESM-MSA":[85],"ESM2.":[87],"These":[88],"are":[90],"processed":[91],"using":[92],"random":[93],"erasing.":[94],"Additionally,":[95],"incorporates":[97],"various":[98],"mechanisms":[100],"within":[101],"its":[102],"residual":[103],"network,":[104],"effectively":[105],"capturing":[106],"long-range":[107],"sequence":[108],"interactions.":[109],"Tested":[110],"multiple":[112],"datasets,":[113],"outperforms":[115,159],"state-of-the-art":[116],"methods,":[117],"including":[118],"DeepInter,":[119],"DeepHomo2.0,":[120],"CDPred,":[122],"key":[124],"metrics":[126],"such":[127],"as":[128],"top1,":[129],"top10,":[130],"top50,":[131],"topL/10,":[132],"topL/5":[134],"precision":[137,152],"(L:":[138],"Length":[139],"monomer":[142],"homodimer).":[144],"Furthermore,":[145],"experimental":[146],"results":[147],"indicate":[148],"that":[149,160],"mean":[151],"topL/2":[154],"predicted":[155],"AlphaFold2-multimer.":[162]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
