{"id":"https://openalex.org/W3121281384","doi":"https://doi.org/10.1093/bib/bbaa397","title":"NCBRPred: predicting nucleic acid binding residues in proteins based on multilabel learning","display_name":"NCBRPred: predicting nucleic acid binding residues in proteins based on multilabel learning","publication_year":2020,"publication_date":"2020-12-03","ids":{"openalex":"https://openalex.org/W3121281384","doi":"https://doi.org/10.1093/bib/bbaa397","mag":"3121281384","pmid":"https://pubmed.ncbi.nlm.nih.gov/33454744"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa397","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa397","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/A5112480733","display_name":"Jun Zhang","orcid":"https://orcid.org/0009-0003-8185-4517"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Zhang","raw_affiliation_strings":["Computer Science and Technology with Harbin Institute of Technology, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"Computer Science and Technology with Harbin Institute of Technology, Shenzhen, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101895423","display_name":"Qingcai Chen","orcid":"https://orcid.org/0000-0001-8473-7293"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingcai Chen","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100395591","display_name":"Bin Liu","orcid":"https://orcid.org/0000-0003-3685-9469"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bin Liu","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, China","institution_ids":["https://openalex.org/I204983213"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100395591"],"corresponding_institution_ids":["https://openalex.org/I204983213"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.0865,"has_fulltext":false,"cited_by_count":69,"citation_normalized_percentile":{"value":0.87998105,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"22","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991999864578247,"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":0.9987999796867371,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/nucleic-acid","display_name":"Nucleic acid","score":0.7910885214805603},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6735429763793945},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6107715964317322},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5993506908416748},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.47663578391075134},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4338802695274353},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4283466637134552},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.27988460659980774},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24197903275489807},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21562272310256958}],"concepts":[{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.7910885214805603},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6735429763793945},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6107715964317322},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5993506908416748},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47663578391075134},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4338802695274353},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4283466637134552},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.27988460659980774},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24197903275489807},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21562272310256958},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","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},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","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}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013194","descriptor_name":"Staining and Labeling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013194","descriptor_name":"Staining and Labeling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013194","descriptor_name":"Staining and Labeling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa397","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa397","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33454744","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33454744","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G3425444037","display_name":null,"funder_award_id":"2018AAA0100100","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4864480503","display_name":null,"funder_award_id":"61822306","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6876496325","display_name":null,"funder_award_id":"JQ19019","funder_id":"https://openalex.org/F4320322919","funder_display_name":"Natural Science Foundation of Beijing Municipality"},{"id":"https://openalex.org/G74711194","display_name":null,"funder_award_id":"61732012","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G75457812","display_name":null,"funder_award_id":"61672184","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8031058355","display_name":null,"funder_award_id":"61861146002","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322919","display_name":"Natural Science Foundation of Beijing Municipality","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1543773936","https://openalex.org/W1901968134","https://openalex.org/W1969156759","https://openalex.org/W1971894358","https://openalex.org/W1973356821","https://openalex.org/W1997401305","https://openalex.org/W1997535872","https://openalex.org/W2026690931","https://openalex.org/W2051210555","https://openalex.org/W2054964748","https://openalex.org/W2055043387","https://openalex.org/W2062296203","https://openalex.org/W2064675550","https://openalex.org/W2094173044","https://openalex.org/W2098412979","https://openalex.org/W2103505761","https://openalex.org/W2115547583","https://openalex.org/W2119493141","https://openalex.org/W2119948329","https://openalex.org/W2130479394","https://openalex.org/W2131474431","https://openalex.org/W2149997286","https://openalex.org/W2157331557","https://openalex.org/W2157806713","https://openalex.org/W2158714788","https://openalex.org/W2167884443","https://openalex.org/W2168055922","https://openalex.org/W2168272116","https://openalex.org/W2198630282","https://openalex.org/W2271840356","https://openalex.org/W2311607323","https://openalex.org/W2545255051","https://openalex.org/W2566370974","https://openalex.org/W2582176104","https://openalex.org/W2762448613","https://openalex.org/W2772865572","https://openalex.org/W2780936345","https://openalex.org/W2807540482","https://openalex.org/W2892720054","https://openalex.org/W2905281057","https://openalex.org/W2951748044","https://openalex.org/W2972223935","https://openalex.org/W2972411752","https://openalex.org/W3007616265","https://openalex.org/W6683258052","https://openalex.org/W6694517276","https://openalex.org/W6698064614","https://openalex.org/W6732748968"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W1971444612","https://openalex.org/W1543504406","https://openalex.org/W633173308","https://openalex.org/W2802691951","https://openalex.org/W2745001401","https://openalex.org/W2383750441","https://openalex.org/W4321353415","https://openalex.org/W1572021523","https://openalex.org/W2061946247"],"abstract_inverted_index":{"The":[0,167],"interactions":[1,68,127],"between":[2],"proteins":[3,28],"and":[4,15,131,148,169],"nucleic":[5,23,54,104,193],"acid":[6,24,55,105,194],"sequences":[7],"play":[8],"many":[9],"important":[10],"roles":[11],"in":[12,27,58],"gene":[13,37],"expression":[14],"some":[16],"cellular":[17],"activities.":[18],"Accurate":[19],"prediction":[20],"of":[21,33,173],"the":[22,31,34,53,66,70,103,110,117,125,129],"binding":[25,56,106,195],"residues":[26,57,71,107],"will":[29,185],"facilitate":[30],"research":[32],"protein":[35],"functions,":[36],"expression,":[38],"drug":[39],"design,":[40],"etc.":[41],"In":[42,90],"this":[43,88,91,133],"regard,":[44],"several":[45],"computational":[46,95],"methods":[47,62,76],"have":[48],"been":[49],"proposed":[50,100],"to":[51,86,101,123],"predict":[52,102],"proteins.":[59],"However,":[60],"these":[61,75],"cannot":[63],"satisfactorily":[64],"measure":[65],"global":[67,126],"among":[69,128],"along":[72],"protein.":[73],"Furthermore,":[74],"are":[77,175],"suffering":[78],"cross-prediction":[79],"problem,":[80],"new":[81,94],"strategies":[82],"should":[83],"be":[84],"explored":[85],"solve":[87],"problem.":[89],"study,":[92],"a":[93,136,170,187],"method":[96],"called":[97],"NCBRPred":[98,115,154,174,184],"was":[99],"based":[108],"on":[109,142],"multilabel":[111,137],"sequence":[112],"labeling":[113],"model.":[114],"used":[116,145],"bidirectional":[118],"Gated":[119],"Recurrent":[120],"Units":[121],"(BiGRUs)":[122],"capture":[124],"residues,":[130],"treats":[132],"task":[134],"as":[135],"learning":[138],"task.":[139],"Experimental":[140],"results":[141,158],"three":[143],"widely":[144],"benchmark":[146],"datasets":[147],"an":[149],"independent":[150],"dataset":[151],"showed":[152],"that":[153,183],"achieved":[155],"higher":[156],"predictive":[157],"with":[159],"lower":[160],"cross-prediction,":[161],"outperforming":[162],"10":[163],"existing":[164],"state-of-the-art":[165],"predictors.":[166],"web-server":[168],"stand-alone":[171],"package":[172],"freely":[176],"available":[177],"at":[178],"http://bliulab.net/NCBRPred.":[179],"It":[180],"is":[181],"anticipated":[182],"become":[186],"very":[188],"useful":[189],"tool":[190],"for":[191],"identifying":[192],"residues.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":5}],"updated_date":"2026-03-26T15:22:09.906841","created_date":"2025-10-10T00:00:00"}