{"id":"https://openalex.org/W4388052750","doi":"https://doi.org/10.1109/access.2023.3328960","title":"EmbedCaps-DBP: Predicting DNA-Binding Proteins Using Protein Sequence Embedding and Capsule Network","display_name":"EmbedCaps-DBP: Predicting DNA-Binding Proteins Using Protein Sequence Embedding and Capsule Network","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W4388052750","doi":"https://doi.org/10.1109/access.2023.3328960"},"language":"en","primary_location":{"id":"doi:10.1109/access.2023.3328960","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2023.3328960","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/10302268.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/10302268.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110072338","display_name":"Muhammad Khaerul Naim","orcid":null},"institutions":[{"id":"https://openalex.org/I134635517","display_name":"Bandung Institute of Technology","ror":"https://ror.org/00apj8t60","country_code":"ID","type":"education","lineage":["https://openalex.org/I134635517"]}],"countries":["ID"],"is_corresponding":true,"raw_author_name":"Muhammad Khaerul Naim","raw_affiliation_strings":["School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia","Department of Informatics Engineering, Universal University, Batam, Indonesia"],"raw_orcid":"https://orcid.org/0000-0001-9330-5863","affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia","institution_ids":["https://openalex.org/I134635517"]},{"raw_affiliation_string":"Department of Informatics Engineering, Universal University, Batam, Indonesia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010526830","display_name":"Tati Latifah Mengko","orcid":"https://orcid.org/0000-0003-4698-3017"},"institutions":[{"id":"https://openalex.org/I134635517","display_name":"Bandung Institute of Technology","ror":"https://ror.org/00apj8t60","country_code":"ID","type":"education","lineage":["https://openalex.org/I134635517"]}],"countries":["ID"],"is_corresponding":false,"raw_author_name":"Tati Rajab Mengko","raw_affiliation_strings":["School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia"],"raw_orcid":"https://orcid.org/0000-0003-4698-3017","affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia","institution_ids":["https://openalex.org/I134635517"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004279340","display_name":"Rukman Hertadi","orcid":"https://orcid.org/0000-0002-4352-5830"},"institutions":[{"id":"https://openalex.org/I134635517","display_name":"Bandung Institute of Technology","ror":"https://ror.org/00apj8t60","country_code":"ID","type":"education","lineage":["https://openalex.org/I134635517"]}],"countries":["ID"],"is_corresponding":false,"raw_author_name":"Rukman Hertadi","raw_affiliation_strings":["Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Bandung, Indonesia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Bandung, Indonesia","institution_ids":["https://openalex.org/I134635517"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021128017","display_name":"Ayu Purwarianti","orcid":"https://orcid.org/0000-0002-5016-3700"},"institutions":[{"id":"https://openalex.org/I134635517","display_name":"Bandung Institute of Technology","ror":"https://ror.org/00apj8t60","country_code":"ID","type":"education","lineage":["https://openalex.org/I134635517"]}],"countries":["ID"],"is_corresponding":false,"raw_author_name":"Ayu Purwarianti","raw_affiliation_strings":["School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia","Center for Artificial Intelligence (U-CoE AI-VLB), Bandung Institute of Technology, Bandung, Indonesia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia","institution_ids":["https://openalex.org/I134635517"]},{"raw_affiliation_string":"Center for Artificial Intelligence (U-CoE AI-VLB), Bandung Institute of Technology, Bandung, Indonesia","institution_ids":["https://openalex.org/I134635517"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082779089","display_name":"Meredita Susanty","orcid":"https://orcid.org/0000-0002-7948-6693"},"institutions":[{"id":"https://openalex.org/I134635517","display_name":"Bandung Institute of Technology","ror":"https://ror.org/00apj8t60","country_code":"ID","type":"education","lineage":["https://openalex.org/I134635517"]},{"id":"https://openalex.org/I194343955","display_name":"Pertamina (Indonesia)","ror":"https://ror.org/002hgm057","country_code":"ID","type":"company","lineage":["https://openalex.org/I194343955"]},{"id":"https://openalex.org/I4387153834","display_name":"Universitas Pertamina","ror":"https://ror.org/0266sez77","country_code":null,"type":"education","lineage":["https://openalex.org/I194343955","https://openalex.org/I4387153834"]}],"countries":["ID"],"is_corresponding":false,"raw_author_name":"Meredita Susanty","raw_affiliation_strings":["School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia","Department of Computer Science, Pertamina University, Jakarta, Indonesia"],"raw_orcid":"https://orcid.org/0000-0002-7948-6693","affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia","institution_ids":["https://openalex.org/I134635517"]},{"raw_affiliation_string":"Department of Computer Science, Pertamina University, Jakarta, Indonesia","institution_ids":["https://openalex.org/I194343955","https://openalex.org/I4387153834"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5110072338"],"corresponding_institution_ids":["https://openalex.org/I134635517"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":1.4825,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.82621699,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"11","issue":null,"first_page":"121256","last_page":"121268"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9997000098228455,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9997000098228455,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9962999820709229,"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":0.5491833090782166},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5413041710853577},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4911791980266571},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45730167627334595},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.43401122093200684},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.26975202560424805},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2630043029785156},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1876242458820343},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.17447152733802795}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5491833090782166},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5413041710853577},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4911791980266571},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45730167627334595},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.43401122093200684},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.26975202560424805},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2630043029785156},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1876242458820343},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.17447152733802795}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2023.3328960","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2023.3328960","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/10302268.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:75397987317b4cd794d15e610d1c1fec","is_oa":true,"landing_page_url":"https://doaj.org/article/75397987317b4cd794d15e610d1c1fec","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 11, Pp 121256-121268 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2023.3328960","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2023.3328960","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/10302268.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3236474954","display_name":null,"funder_award_id":"FR742022288602","funder_id":"https://openalex.org/F4320328515","funder_display_name":"Lembaga Pengelola Dana Pendidikan"}],"funders":[{"id":"https://openalex.org/F4320328515","display_name":"Lembaga Pengelola Dana Pendidikan","ror":null},{"id":"https://openalex.org/F4320329091","display_name":"Institut Teknologi Bandung","ror":"https://ror.org/00apj8t60"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388052750.pdf","grobid_xml":"https://content.openalex.org/works/W4388052750.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W1501531009","https://openalex.org/W1533958831","https://openalex.org/W1968682237","https://openalex.org/W1983057459","https://openalex.org/W1997401305","https://openalex.org/W2009470087","https://openalex.org/W2010688088","https://openalex.org/W2012834844","https://openalex.org/W2018327163","https://openalex.org/W2030922238","https://openalex.org/W2061293154","https://openalex.org/W2070980386","https://openalex.org/W2090561245","https://openalex.org/W2094764962","https://openalex.org/W2114535505","https://openalex.org/W2121090558","https://openalex.org/W2143887102","https://openalex.org/W2155770902","https://openalex.org/W2158714788","https://openalex.org/W2168970921","https://openalex.org/W2173591891","https://openalex.org/W2173801226","https://openalex.org/W2227395312","https://openalex.org/W2470414691","https://openalex.org/W2557383173","https://openalex.org/W2766430481","https://openalex.org/W2769306988","https://openalex.org/W2781086737","https://openalex.org/W2785994986","https://openalex.org/W2796206050","https://openalex.org/W2804549231","https://openalex.org/W2888408766","https://openalex.org/W2896457183","https://openalex.org/W2909686100","https://openalex.org/W2947980028","https://openalex.org/W2948484546","https://openalex.org/W2955151077","https://openalex.org/W2959124424","https://openalex.org/W2963703618","https://openalex.org/W2965626518","https://openalex.org/W2969768983","https://openalex.org/W2995514860","https://openalex.org/W3011574394","https://openalex.org/W3019166713","https://openalex.org/W3040052015","https://openalex.org/W3049692992","https://openalex.org/W3080498684","https://openalex.org/W3088409176","https://openalex.org/W3118936575","https://openalex.org/W3121000782","https://openalex.org/W3136918052","https://openalex.org/W3146944767","https://openalex.org/W3161612534","https://openalex.org/W3163595068","https://openalex.org/W3166730506","https://openalex.org/W3177500196","https://openalex.org/W3179485843","https://openalex.org/W3202431085","https://openalex.org/W4205773061","https://openalex.org/W4206087583","https://openalex.org/W4206247924","https://openalex.org/W4206948363","https://openalex.org/W4210535996","https://openalex.org/W4210997669","https://openalex.org/W4214656865","https://openalex.org/W4220667786","https://openalex.org/W4220952154","https://openalex.org/W4224095040","https://openalex.org/W4300861364","https://openalex.org/W4308823166","https://openalex.org/W6743446608","https://openalex.org/W6748053814","https://openalex.org/W6755207826","https://openalex.org/W6798272402"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2081900870","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2966686650"],"abstract_inverted_index":{"DNA-binding":[0,18],"interactions":[1],"are":[2,38],"an":[3],"essential":[4],"biological":[5],"activity":[6],"with":[7,25],"important":[8,108],"functions,":[9],"such":[10,29,113],"as":[11,30,114,137],"DNA":[12],"replication,":[13],"transcription,":[14],"repair,":[15],"and":[16,33,49,69,93,118,148,160,170],"recombination.":[17],"proteins":[19],"(DBPs)":[20],"have":[21,55,65,121],"been":[22,123],"strongly":[23],"associated":[24],"various":[26],"human":[27],"diseases,":[28],"asthma,":[31],"cancer,":[32],"HIV/AIDS.":[34],"Therefore,":[35],"some":[36],"DBPs":[37],"used":[39,56,86,132],"in":[40,126,146],"the":[41],"pharmaceutical":[42],"industry":[43],"to":[44,59,95],"produce":[45,70],"antibiotics,":[46],"anticancer":[47],"drugs,":[48],"anti-inflammatory":[50],"drugs.":[51],"Most":[52],"previous":[53],"methods":[54,64,105],"evolutionary":[57],"information":[58,109],"predict":[60],"DBPs.":[61,185],"However,":[62],"these":[63],"high":[66],"computing":[67],"costs":[68],"unsatisfactory":[71],"results.":[72],"This":[73],"study":[74],"presents":[75],"EmbedCaps-DBP,":[76],"a":[77,133,138,165,181],"new":[78],"method":[79,179],"for":[80],"improving":[81],"DBP":[82],"prediction.":[83],"First,":[84],"we":[85,131],"three":[87],"protein":[88,101,127],"sequence":[89],"embeddings":[90],"(ProtT5,":[91],"ESM-1b,":[92],"ESM-2)":[94],"extract":[96],"learned":[97],"feature":[98],"representations":[99],"from":[100],"sequences.":[102],"Those":[103],"embedding":[104],"can":[106],"capture":[107],"about":[110],"amino":[111],"acids,":[112],"biophysics,":[115],"biochemistry,":[116],"structure,":[117],"domains,":[119],"that":[120,176],"not":[122],"fully":[124],"utilized":[125],"annotation":[128],"tasks.":[129],"Then,":[130],"1D-capsule":[134],"network":[135],"(CapsNet)":[136],"classifier.":[139],"EmbedCaps-DBP":[140,156],"significantly":[141],"outperformed":[142],"all":[143],"existing":[144],"classifiers":[145],"training":[147],"independent":[149,154],"datasets.":[150],"Based":[151],"on":[152,168],"two":[153],"datasets,":[155],"(ProtT5)":[157],"achieved":[158],"12.65%":[159],"0.33%":[161],"higher":[162],"accuracies":[163],"than":[164],"recent":[166],"predictor":[167,183],"PDB2272":[169],"PDB186,":[171],"respectively.":[172],"These":[173],"results":[174],"indicate":[175],"our":[177],"proposed":[178],"is":[180],"promising":[182],"of":[184]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
