{"id":"https://openalex.org/W2616608982","doi":"https://doi.org/10.1504/ijdmb.2017.10005211","title":"Prediction of DNA-binding residues from sequence information using convolutional neural network","display_name":"Prediction of DNA-binding residues from sequence information using convolutional neural network","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2616608982","doi":"https://doi.org/10.1504/ijdmb.2017.10005211","mag":"2616608982"},"language":"en","primary_location":{"id":"doi:10.1504/ijdmb.2017.10005211","is_oa":false,"landing_page_url":"https://doi.org/10.1504/ijdmb.2017.10005211","pdf_url":null,"source":{"id":"https://openalex.org/S35771696","display_name":"International Journal of Data Mining and Bioinformatics","issn_l":"1748-5673","issn":["1748-5673","1748-5681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310317825","host_organization_name":"Inderscience Publishers","host_organization_lineage":["https://openalex.org/P4310317825"],"host_organization_lineage_names":["Inderscience Publishers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Data Mining and Bioinformatics","raw_type":"journal-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/A5100608721","display_name":"Hongpeng Wang","orcid":"https://orcid.org/0000-0001-8108-2674"},"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":"Hongpeng Wang","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062168574","display_name":"Lin Gui","orcid":"https://orcid.org/0000-0002-8054-9524"},"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":"Lin Gui","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016391596","display_name":"Qin Lu","orcid":"https://orcid.org/0000-0002-9092-2476"},"institutions":[{"id":"https://openalex.org/I14243506","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98","country_code":"HK","type":"education","lineage":["https://openalex.org/I14243506"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Qin Lu","raw_affiliation_strings":["Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong","institution_ids":["https://openalex.org/I14243506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100616656","display_name":"Ruifeng Xu","orcid":"https://orcid.org/0009-0000-4425-0763"},"institutions":[{"id":"https://openalex.org/I158809036","display_name":"Shenzhen Institute of Information Technology","ror":"https://ror.org/03wrf9427","country_code":"CN","type":"education","lineage":["https://openalex.org/I158809036"]},{"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":"Ruifeng Xu","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China; Shenzhen Engineering Laboratory of Performance Robots at Digital Stage, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, China","School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","Shenzhen Engineering Laboratory of Performance Robots at Digital Stage, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China; Shenzhen Engineering Laboratory of Performance Robots at Digital Stage, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, China","institution_ids":["https://openalex.org/I158809036"]},{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"Shenzhen Engineering Laboratory of Performance Robots at Digital Stage, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048243922","display_name":"Jiyun Zhou","orcid":"https://orcid.org/0000-0002-2145-2976"},"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"]},{"id":"https://openalex.org/I14243506","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98","country_code":"HK","type":"education","lineage":["https://openalex.org/I14243506"]},{"id":"https://openalex.org/I182722699","display_name":"Shenzhen Polytechnic","ror":"https://ror.org/00d2w9g53","country_code":"CN","type":"education","lineage":["https://openalex.org/I182722699"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Jiyun Zhou","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China; Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong","Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong","School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China; Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong","institution_ids":["https://openalex.org/I14243506","https://openalex.org/I182722699"]},{"raw_affiliation_string":"Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong","institution_ids":["https://openalex.org/I14243506"]},{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I204983213"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100608721"],"corresponding_institution_ids":["https://openalex.org/I204983213"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.04365648,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"2","first_page":"132","last_page":"132"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9998000264167786,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9995999932289124,"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/convolutional-neural-network","display_name":"Convolutional neural network","score":0.7052952647209167},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.6677454710006714},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.6200227737426758},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.597160816192627},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5195322632789612},{"id":"https://openalex.org/keywords/discriminant","display_name":"Discriminant","score":0.47771120071411133},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.45515650510787964},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4476897418498993},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4438198208808899},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.43812376260757446},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4337177276611328},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40755560994148254},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3442012071609497},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2144622504711151}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7052952647209167},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.6677454710006714},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6200227737426758},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.597160816192627},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5195322632789612},{"id":"https://openalex.org/C78397625","wikidata":"https://www.wikidata.org/wiki/Q192487","display_name":"Discriminant","level":2,"score":0.47771120071411133},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.45515650510787964},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4476897418498993},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4438198208808899},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.43812376260757446},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4337177276611328},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40755560994148254},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3442012071609497},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2144622504711151},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1504/ijdmb.2017.10005211","is_oa":false,"landing_page_url":"https://doi.org/10.1504/ijdmb.2017.10005211","pdf_url":null,"source":{"id":"https://openalex.org/S35771696","display_name":"International Journal of Data Mining and Bioinformatics","issn_l":"1748-5673","issn":["1748-5673","1748-5681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310317825","host_organization_name":"Inderscience Publishers","host_organization_lineage":["https://openalex.org/P4310317825"],"host_organization_lineage_names":["Inderscience Publishers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Data Mining and Bioinformatics","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.7400000095367432}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W311077022","https://openalex.org/W1019830208","https://openalex.org/W1491553314","https://openalex.org/W1543773936","https://openalex.org/W1566376227","https://openalex.org/W1608094292","https://openalex.org/W1971894358","https://openalex.org/W1976521702","https://openalex.org/W1981482769","https://openalex.org/W1997401305","https://openalex.org/W1998518361","https://openalex.org/W2003916208","https://openalex.org/W2012834844","https://openalex.org/W2013734705","https://openalex.org/W2038670706","https://openalex.org/W2051167924","https://openalex.org/W2089716128","https://openalex.org/W2092358369","https://openalex.org/W2096986143","https://openalex.org/W2099485600","https://openalex.org/W2099886875","https://openalex.org/W2102154371","https://openalex.org/W2117128942","https://openalex.org/W2117130368","https://openalex.org/W2119109353","https://openalex.org/W2119948329","https://openalex.org/W2123525093","https://openalex.org/W2128533758","https://openalex.org/W2133312664","https://openalex.org/W2134923281","https://openalex.org/W2141125852","https://openalex.org/W2141149420","https://openalex.org/W2142529984","https://openalex.org/W2143887102","https://openalex.org/W2144354855","https://openalex.org/W2144792857","https://openalex.org/W2147285856","https://openalex.org/W2149997286","https://openalex.org/W2152116196","https://openalex.org/W2154302035","https://openalex.org/W2156136208","https://openalex.org/W2156163116","https://openalex.org/W2156690214","https://openalex.org/W2160800572","https://openalex.org/W2168208027","https://openalex.org/W2576351606","https://openalex.org/W2618530766","https://openalex.org/W2911964244","https://openalex.org/W2963457143"],"related_works":["https://openalex.org/W3170299350","https://openalex.org/W2073661767","https://openalex.org/W2143211236","https://openalex.org/W2380185347","https://openalex.org/W2370034659","https://openalex.org/W2159636084","https://openalex.org/W2610941444","https://openalex.org/W2117168988","https://openalex.org/W2154430121","https://openalex.org/W2103777723"],"abstract_inverted_index":{"Most":[0],"DNA-binding":[1,141],"residue":[2,142],"prediction":[3],"methods":[4],"overlooked":[5],"the":[6,13,24,59,102,114],"motif":[7,25,44,61,77,110,138],"features":[8,26,64,78,83,111,139],"which":[9,116],"are":[10],"important":[11,118,137],"for":[12,27,140],"recognition":[14],"between":[15],"protein":[16],"and":[17,65,73,84,92],"DNA.":[18],"In":[19],"order":[20],"to":[21,32,41,54,135],"efficiently":[22],"use":[23,33],"prediction,":[28],"we":[29],"first":[30],"propose":[31,48],"Convolutional":[34],"Neural":[35],"Network":[36],"(CNN)":[37],"in":[38,120],"deep":[39],"learning":[40],"extract":[42,136],"discriminant":[43,125],"features.":[45,67,86],"We":[46,105],"then":[47],"a":[49],"neural":[50],"network":[51],"classifier,":[52],"referred":[53],"as":[55],"CNNsite,":[56],"by":[57,113],"combining":[58],"extracted":[60],"features,":[62],"sequence":[63,82],"evolutionary":[66,85],"The":[68,87],"evaluation":[69,88],"on":[70,89],"PDNA-62,":[71,90],"PDNA-224":[72,91],"TR-265":[74],"shows":[75,97],"that":[76,98,108,129],"perform":[79],"better":[80],"than":[81],"an":[93],"independent":[94],"data":[95],"set":[96],"CNNsite":[99,130],"also":[100,106],"outperforms":[101],"previous":[103],"methods.":[104],"show":[107],"many":[109],"composed":[112],"residues":[115],"play":[117],"roles":[119],"DNA-protein":[121],"interactions":[122],"have":[123],"large":[124],"powers.":[126],"It":[127],"indicates":[128],"has":[131],"very":[132],"good":[133],"ability":[134],"prediction.":[143]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}