{"id":"https://openalex.org/W4390991996","doi":"https://doi.org/10.1109/bibm58861.2023.10385509","title":"ESM-NBR: fast and accurate nucleic acid-binding residue prediction via protein language model feature representation and multi-task learning","display_name":"ESM-NBR: fast and accurate nucleic acid-binding residue prediction via protein language model feature representation and multi-task learning","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390991996","doi":"https://doi.org/10.1109/bibm58861.2023.10385509"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385509","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385509","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5028448669","display_name":"Wenwu Zeng","orcid":"https://orcid.org/0009-0002-6104-0527"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenwu Zeng","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","College of Computer Science and Electronic Engineering, Hunan University, Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","institution_ids":["https://openalex.org/I16609230"]},{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113063693","display_name":"Dafeng Lv","orcid":null},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dafeng Lv","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","College of Computer Science and Electronic Engineering, Hunan University, Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","institution_ids":["https://openalex.org/I16609230"]},{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100362298","display_name":"Xuan Liu","orcid":"https://orcid.org/0000-0002-1652-2466"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuan Liu","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","College of Computer Science and Electronic Engineering, Hunan University, Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","institution_ids":["https://openalex.org/I16609230"]},{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009477401","display_name":"Guo Chen","orcid":"https://orcid.org/0000-0002-6069-6869"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guo Chen","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","College of Computer Science and Electronic Engineering, Hunan University, Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","institution_ids":["https://openalex.org/I16609230"]},{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100430634","display_name":"Wenjuan Liu","orcid":"https://orcid.org/0000-0001-9746-3041"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenjuan Liu","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","College of Computer Science and Electronic Engineering, Hunan University, Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","institution_ids":["https://openalex.org/I16609230"]},{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108008219","display_name":"Shaoliang Peng","orcid":"https://orcid.org/0000-0002-4647-2615"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaoliang Peng","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","College of Computer Science and Electronic Engineering, Hunan University, Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Hunan,China","institution_ids":["https://openalex.org/I16609230"]},{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I16609230"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"76","last_page":"81"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9993000030517578,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9993000030517578,"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":0.9986000061035156,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9984999895095825,"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":0.6782657504081726},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5625189542770386},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5466405153274536},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5102863311767578},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.46696406602859497},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4638040065765381},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.46186500787734985},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.440021812915802},{"id":"https://openalex.org/keywords/feature-extraction","display_name":"Feature extraction","score":0.43816694617271423},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.42748168110847473},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4171372354030609},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.4128953814506531},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.13990962505340576},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10267698764801025}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6782657504081726},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5625189542770386},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5466405153274536},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5102863311767578},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.46696406602859497},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4638040065765381},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.46186500787734985},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.440021812915802},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.43816694617271423},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.42748168110847473},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4171372354030609},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.4128953814506531},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.13990962505340576},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10267698764801025},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385509","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385509","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","score":0.6200000047683716,"id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1969528530","https://openalex.org/W2003893812","https://openalex.org/W2008056655","https://openalex.org/W2018661561","https://openalex.org/W2051210555","https://openalex.org/W2084014179","https://openalex.org/W2090081965","https://openalex.org/W2102945860","https://openalex.org/W2133036743","https://openalex.org/W2152178770","https://openalex.org/W2158714788","https://openalex.org/W2582176104","https://openalex.org/W2807540482","https://openalex.org/W2892720054","https://openalex.org/W2933350524","https://openalex.org/W2963608065","https://openalex.org/W3009202743","https://openalex.org/W3010387158","https://openalex.org/W3027554922","https://openalex.org/W3042914343","https://openalex.org/W3121281384","https://openalex.org/W3126876258","https://openalex.org/W3136918052","https://openalex.org/W3146944767","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3208957581","https://openalex.org/W3213101281","https://openalex.org/W4205989901","https://openalex.org/W4210262283","https://openalex.org/W4281790889","https://openalex.org/W4283011532","https://openalex.org/W4297807322","https://openalex.org/W4311456810","https://openalex.org/W4319083882","https://openalex.org/W4327550249","https://openalex.org/W4362515116","https://openalex.org/W4378781940","https://openalex.org/W4388024559","https://openalex.org/W6774110404","https://openalex.org/W6851775633"],"related_works":["https://openalex.org/W2965546495","https://openalex.org/W4389116644","https://openalex.org/W2167155152","https://openalex.org/W3208297503","https://openalex.org/W3119773509","https://openalex.org/W2889153461","https://openalex.org/W2964117661","https://openalex.org/W4388405611","https://openalex.org/W2619127353","https://openalex.org/W4309346246"],"abstract_inverted_index":{"Protein-nucleic":[0],"acid":[1],"interactions":[2],"play":[3],"a":[4,9,21,47,80,196],"very":[5],"important":[6],"role":[7],"in":[8,24],"variety":[10],"of":[11,16,86,106,127,151,168,186,191,199,219],"biological":[12,71],"activities.":[13],"Accurate":[14],"identification":[15],"nucleic":[17,39],"acid-binding":[18,40],"residues":[19,110,149],"is":[20,55,98,203],"critical":[22],"step":[23],"understanding":[25],"the":[26,62,124,141,144,169,177,183,209,217],"interaction":[27],"mechanisms.":[28],"Although":[29],"many":[30],"computationally":[31],"based":[32],"methods":[33,193],"have":[34],"been":[35],"developed":[36],"to":[37,68,100],"predict":[38],"residues,":[41],"challenges":[42],"remain.":[43],"In":[44,57],"this":[45],"study,":[46],"fast":[48],"and":[49,93,103,108,153,163,216],"accurate":[50],"sequence-based":[51],"method,":[52],"called":[53],"ESM-NBR,":[54,58],"proposed.":[56],"we":[59],"first":[60],"use":[61,226],"large":[63],"protein":[64,76,197],"language":[65],"model":[66,84,137],"ESM2":[67,112,128],"extract":[69],"discriminative":[70],"properties":[72],"feature":[73,113,129],"representation":[74,130],"from":[75],"primary":[77],"sequences;":[78],"then,":[79],"multi-task":[81],"deep":[82],"learning":[83],"composed":[85],"stacked":[87],"bidirectional":[88],"long":[89],"short-term":[90],"memory":[91],"(BiLSTM)":[92],"multi-layer":[94],"perceptron":[95],"(MLP)":[96],"networks":[97],"employed":[99],"explore":[101],"common":[102],"private":[104],"information":[105],"DNA-":[107],"RNA-binding":[109],"with":[111],"as":[114],"input.":[115],"Experimental":[116],"results":[117],"on":[118,155],"benchmark":[119],"data":[120,218],"sets":[121],"demonstrate":[122],"that":[123,190],"prediction":[125,150,184],"performance":[126],"comprehensively":[131],"outperforms":[132],"evolutionary":[133],"information-based":[134],"hidden":[135],"Markov":[136],"(HMM)":[138],"features.":[139],"Meanwhile,":[140],"ESM-NBR":[142,187,220],"obtains":[143],"MCC":[145],"values":[146],"for":[147,195,224],"DNA-binding":[148],"0.427":[152],"0.391":[154],"two":[156],"independent":[157],"test":[158],"sets,":[159],"which":[160,202],"are":[161,221],"18.61":[162],"10.45%":[164],"higher":[165],"than":[166,208],"those":[167],"second-best":[170],"methods,":[171],"respectively.":[172],"Moreover,":[173],"by":[174],"completely":[175],"discarding":[176],"time-cost":[178],"multiple":[179],"sequence":[180,198],"alignment":[181],"process,":[182],"speed":[185],"far":[188],"exceeds":[189],"existing":[192],"(5.52s":[194],"length":[200],"500,":[201],"about":[204],"16":[205],"times":[206],"faster":[207],"second-fastest":[210],"method).":[211],"A":[212],"user-friendly":[213],"standalone":[214],"package":[215],"freely":[222],"available":[223],"academic":[225],"at:":[227],"https://github.com/wwzll123/ESM-NBR.":[228]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":6}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2024-01-19T00:00:00"}
