{"id":"https://openalex.org/W2892720054","doi":"https://doi.org/10.1093/bioinformatics/bty756","title":"Improving the prediction of protein\u2013nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods","display_name":"Improving the prediction of protein\u2013nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods","publication_year":2018,"publication_date":"2018-08-29","ids":{"openalex":"https://openalex.org/W2892720054","doi":"https://doi.org/10.1093/bioinformatics/bty756","mag":"2892720054","pmid":"https://pubmed.ncbi.nlm.nih.gov/30169574"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty756","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty756","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041570778","display_name":"Hong Su","orcid":"https://orcid.org/0000-0003-2842-5003"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong Su","raw_affiliation_strings":["School of Mathematical Sciences, Nankai University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107904995","display_name":"Mengchen Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengchen Liu","raw_affiliation_strings":["School of Mathematical Sciences, Nankai University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021650927","display_name":"Saisai Sun","orcid":"https://orcid.org/0009-0004-6090-3030"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Saisai Sun","raw_affiliation_strings":["School of Mathematical Sciences, Nankai University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020435329","display_name":"Zhenling Peng","orcid":"https://orcid.org/0000-0003-0303-6693"},"institutions":[{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhenling Peng","raw_affiliation_strings":["Center for Applied Mathematics, Tianjin University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Applied Mathematics, Tianjin University, Tianjin, China","institution_ids":["https://openalex.org/I162868743"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107636936","display_name":"Jianyi Yang","orcid":"https://orcid.org/0000-0003-2912-7737"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianyi Yang","raw_affiliation_strings":["School of Mathematical Sciences, Nankai University, Tianjin, China"],"raw_orcid":"https://orcid.org/0000-0003-2912-7737","affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5020435329","https://openalex.org/A5107636936"],"corresponding_institution_ids":["https://openalex.org/I162868743","https://openalex.org/I205237279"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":4.6623,"has_fulltext":false,"cited_by_count":105,"citation_normalized_percentile":{"value":0.95678932,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"35","issue":"6","first_page":"930","last_page":"936"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6323000192642212,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6323000192642212,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.19210000336170197,"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":0.09189999848604202,"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/nucleic-acid","display_name":"Nucleic acid","score":0.6716077327728271},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6031114459037781},{"id":"https://openalex.org/keywords/consensus-sequence","display_name":"Consensus sequence","score":0.518691897392273},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5125224590301514},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4921802580356598},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3247172236442566},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.25516635179519653},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23787838220596313},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.23199701309204102},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.21835297346115112}],"concepts":[{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.6716077327728271},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6031114459037781},{"id":"https://openalex.org/C54985914","wikidata":"https://www.wikidata.org/wiki/Q1295754","display_name":"Consensus sequence","level":4,"score":0.518691897392273},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5125224590301514},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4921802580356598},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3247172236442566},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.25516635179519653},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23787838220596313},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.23199701309204102},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.21835297346115112}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty756","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty756","pdf_url":null,"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:30169574","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30169574","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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G226075021","display_name":null,"funder_award_id":"11501407","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6339323267","display_name":"\u57fa\u4e8e\u6570\u636e\u9a71\u52a8\u7684\u86cb\u767d\u8d28\u4e09\u7ea7\u7ed3\u6784\u9884\u6d4b\u7b97\u6cd5\u7814\u7a76","funder_award_id":"11871290","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G649404935","display_name":null,"funder_award_id":"61873185","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7021288394","display_name":null,"funder_award_id":"(11501306","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8532275144","display_name":null,"funder_award_id":"161003","funder_id":"https://openalex.org/F4320334945","funder_display_name":"Fok Ying Tong Education Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320334945","display_name":"Fok Ying Tong Education Foundation","ror":"https://ror.org/01mv9t934"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"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/W1987134040","https://openalex.org/W1997401305","https://openalex.org/W2018661561","https://openalex.org/W2038842667","https://openalex.org/W2044955175","https://openalex.org/W2051210555","https://openalex.org/W2119493141","https://openalex.org/W2119948329","https://openalex.org/W2128607518","https://openalex.org/W2140538197","https://openalex.org/W2149997286","https://openalex.org/W2153187042","https://openalex.org/W2156136208","https://openalex.org/W2158714788","https://openalex.org/W2168055922","https://openalex.org/W2180891129","https://openalex.org/W2198630282","https://openalex.org/W2544136853","https://openalex.org/W2545255051","https://openalex.org/W2561871078","https://openalex.org/W2582176104","https://openalex.org/W2615136515","https://openalex.org/W2625232369","https://openalex.org/W2752956856","https://openalex.org/W2772865572","https://openalex.org/W2791231776","https://openalex.org/W2804736431","https://openalex.org/W2807540482","https://openalex.org/W6732748968","https://openalex.org/W6746260625","https://openalex.org/W6751324841","https://openalex.org/W7075630220"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W2062208111","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,34,105,163,179],"interactions":[2],"between":[3,142],"protein":[4],"and":[5,75,110,144,152,192],"nucleic":[6,23,38,60,102],"acids":[7,24,32],"play":[8],"a":[9,53,68,76,101],"key":[10],"role":[11],"in":[12,150,177],"various":[13],"biological":[14],"processes.":[15],"Accurate":[16],"recognition":[17],"of":[18,29,36,59,158,168,184],"the":[19,27,57,65,92,156,166,182,188,193],"residues":[20,40,94,146],"that":[21,123],"bind":[22],"can":[25],"facilitate":[26],"study":[28],"uncharacterized":[30],"protein-nucleic":[31],"interactions.":[33],"accuracy":[35],"existing":[37],"acids-binding":[39,61,103],"prediction":[41,58,141],"methods":[42,107,115],"is":[43,165,181],"relatively":[44],"low.":[45],"RESULTS:":[46],"In":[47],"this":[48],"work,":[49],"we":[50],"introduce":[51],"NucBind,":[52],"novel":[54],"method":[55,73,78,190,195],"for":[56],"residues.":[62],"NucBind":[63,124,159],"combines":[64],"predictions":[66],"from":[67,85,100,172],"support":[69],"vector":[70],"machine-based":[71],"ab-initio":[72,138,189],"SVMnuc":[74,80,151,191],"template-based":[77,194],"COACH-D.":[79,196],"was":[81,147],"trained":[82],"with":[83,112,131],"features":[84,170],"three":[86,117,173],"complementary":[87,174,186],"sequence":[88,175],"profiles.":[89],"COACH-D":[90],"predicts":[91],"binding":[93],"based":[95],"on":[96,116],"homologous":[97],"templates":[98],"identified":[99],"library.":[104],"proposed":[106],"were":[108],"assessed":[109],"compared":[111],"other":[113,127,137],"peering":[114],"benchmark":[118],"datasets.":[119],"Experimental":[120],"results":[121],"show":[122],"consistently":[125],"outperforms":[126],"state-of-the-art":[128],"methods.":[129],"Though":[130],"higher":[132],"accuracy,":[133],"similar":[134],"to":[135,160],"many":[136],"methods,":[139],"cross":[140],"DNA":[143],"RNA-binding":[145],"also":[148],"observed":[149],"NucBind.":[153],"We":[154],"attribute":[155],"success":[157],"two":[161,185],"folds.":[162],"first":[164],"utilization":[167],"improved":[169],"extracted":[171],"profiles":[176],"SVMnuc.":[178],"second":[180],"combination":[183],"methods:":[187],"AVAILABILITY":[197],"AND":[198],"IMPLEMENTATION:":[199],"http://yanglab.nankai.edu.cn/NucBind.":[200],"SUPPLEMENTARY":[201],"INFORMATION:":[202],"Supplementary":[203],"data":[204],"are":[205],"available":[206],"at":[207],"Bioinformatics":[208],"online.":[209]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":2}],"updated_date":"2026-08-25T07:29:55.448023","created_date":"2025-10-10T00:00:00"}