{"id":"https://openalex.org/W4200111237","doi":"https://doi.org/10.1093/bib/bbab492","title":"DeepCap-Kcr: accurate identification and investigation of protein lysine crotonylation sites based on capsule network","display_name":"DeepCap-Kcr: accurate identification and investigation of protein lysine crotonylation sites based on capsule network","publication_year":2021,"publication_date":"2021-10-26","ids":{"openalex":"https://openalex.org/W4200111237","doi":"https://doi.org/10.1093/bib/bbab492","pmid":"https://pubmed.ncbi.nlm.nih.gov/34882222"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab492","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab492","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/A5066277166","display_name":"Jhabindra Khanal","orcid":"https://orcid.org/0000-0001-6470-1365"},"institutions":[{"id":"https://openalex.org/I80611190","display_name":"Jeonbuk National University","ror":"https://ror.org/05q92br09","country_code":"KR","type":"education","lineage":["https://openalex.org/I80611190"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jhabindra Khanal","raw_affiliation_strings":["Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea","institution_ids":["https://openalex.org/I80611190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008953921","display_name":"Hilal Tayara","orcid":"https://orcid.org/0000-0001-5678-3479"},"institutions":[{"id":"https://openalex.org/I80611190","display_name":"Jeonbuk National University","ror":"https://ror.org/05q92br09","country_code":"KR","type":"education","lineage":["https://openalex.org/I80611190"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hilal Tayara","raw_affiliation_strings":["School of international Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of international Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea","institution_ids":["https://openalex.org/I80611190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017426085","display_name":"Quan Zou","orcid":"https://orcid.org/0000-0001-6406-1142"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Quan Zou","raw_affiliation_strings":["Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031342322","display_name":"Kil To Chong","orcid":"https://orcid.org/0000-0002-1952-0001"},"institutions":[{"id":"https://openalex.org/I80611190","display_name":"Jeonbuk National University","ror":"https://ror.org/05q92br09","country_code":"KR","type":"education","lineage":["https://openalex.org/I80611190"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Kil To Chong","raw_affiliation_strings":["Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea","Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea","institution_ids":["https://openalex.org/I80611190"]},{"raw_affiliation_string":"Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea","institution_ids":["https://openalex.org/I80611190"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017426085","https://openalex.org/A5031342322"],"corresponding_institution_ids":["https://openalex.org/I150229711","https://openalex.org/I80611190"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.6648,"has_fulltext":false,"cited_by_count":50,"citation_normalized_percentile":{"value":0.91627585,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"23","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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":0.9976999759674072,"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":0.7015671133995056},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6507928371429443},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5663263201713562},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.5613092184066772},{"id":"https://openalex.org/keywords/non-histone-protein","display_name":"Non-histone protein","score":0.5357171297073364},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.520195484161377},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.505774974822998},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48765552043914795},{"id":"https://openalex.org/keywords/lysine","display_name":"Lysine","score":0.46717318892478943},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.41293397545814514},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.324246883392334},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3044058680534363},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.16745945811271667},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14159062504768372},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.0927780270576477}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7015671133995056},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6507928371429443},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5663263201713562},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5613092184066772},{"id":"https://openalex.org/C87026931","wikidata":"https://www.wikidata.org/wiki/Q3408226","display_name":"Non-histone protein","level":4,"score":0.5357171297073364},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.520195484161377},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.505774974822998},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48765552043914795},{"id":"https://openalex.org/C2776016237","wikidata":"https://www.wikidata.org/wiki/Q178430","display_name":"Lysine","level":3,"score":0.46717318892478943},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.41293397545814514},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.324246883392334},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3044058680534363},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.16745945811271667},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14159062504768372},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.0927780270576477}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab492","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab492","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:34882222","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34882222","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":[{"id":"https://metadata.un.org/sdg/3","score":0.6399999856948853,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2147753834","display_name":null,"funder_award_id":"NRF-2017M3C7A1044816","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G4069871152","display_name":null,"funder_award_id":"2020R1A2C2005612","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"}],"funders":[{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":70,"referenced_works":["https://openalex.org/W1875842236","https://openalex.org/W1947481528","https://openalex.org/W1993363553","https://openalex.org/W1995286508","https://openalex.org/W2041877620","https://openalex.org/W2046301798","https://openalex.org/W2055397908","https://openalex.org/W2064675550","https://openalex.org/W2068351971","https://openalex.org/W2088511656","https://openalex.org/W2095705004","https://openalex.org/W2096083625","https://openalex.org/W2115862579","https://openalex.org/W2117514345","https://openalex.org/W2133564696","https://openalex.org/W2148741118","https://openalex.org/W2155653793","https://openalex.org/W2337350186","https://openalex.org/W2409489983","https://openalex.org/W2560129407","https://openalex.org/W2590067952","https://openalex.org/W2593128459","https://openalex.org/W2606879989","https://openalex.org/W2621036017","https://openalex.org/W2748860630","https://openalex.org/W2753004519","https://openalex.org/W2768705872","https://openalex.org/W2797472209","https://openalex.org/W2805827044","https://openalex.org/W2809468490","https://openalex.org/W2883294189","https://openalex.org/W2894451965","https://openalex.org/W2901045238","https://openalex.org/W2901218091","https://openalex.org/W2903682118","https://openalex.org/W2943258252","https://openalex.org/W2962655813","https://openalex.org/W2963703618","https://openalex.org/W2971578602","https://openalex.org/W2976262693","https://openalex.org/W2976711440","https://openalex.org/W2979666105","https://openalex.org/W2991059578","https://openalex.org/W2998913411","https://openalex.org/W3005304875","https://openalex.org/W3006565055","https://openalex.org/W3010697764","https://openalex.org/W3013230828","https://openalex.org/W3027122607","https://openalex.org/W3033045590","https://openalex.org/W3048991675","https://openalex.org/W3089668159","https://openalex.org/W3094567318","https://openalex.org/W3102935795","https://openalex.org/W3108267036","https://openalex.org/W3108295356","https://openalex.org/W3109860017","https://openalex.org/W3110770815","https://openalex.org/W3119855908","https://openalex.org/W3120889166","https://openalex.org/W3134384141","https://openalex.org/W3138964863","https://openalex.org/W3162632405","https://openalex.org/W3162917661","https://openalex.org/W3172531794","https://openalex.org/W3199417536","https://openalex.org/W4206174637","https://openalex.org/W4232658741","https://openalex.org/W4234552385","https://openalex.org/W4240768087"],"related_works":["https://openalex.org/W98379584","https://openalex.org/W2413824894","https://openalex.org/W2025957408","https://openalex.org/W2078222809","https://openalex.org/W2055566470","https://openalex.org/W2067046840","https://openalex.org/W1597494200","https://openalex.org/W2041600075","https://openalex.org/W2411028966","https://openalex.org/W2004477202"],"abstract_inverted_index":{"Lysine":[0],"crotonylation":[1],"(Kcr)":[2],"is":[3,48],"a":[4,16,35,76,81,87,156,196],"posttranslational":[5],"modification":[6],"widely":[7],"detected":[8],"in":[9,19,69,122,132,167],"histone":[10,104],"and":[11,23,34,54,92,105,118,125,176,202],"nonhistone":[12,106],"proteins.":[13,70],"It":[14],"plays":[15],"vital":[17],"role":[18],"human":[20],"disease":[21],"progression":[22],"various":[24],"cellular":[25],"processes,":[26],"including":[27],"cell":[28,30],"cycle,":[29],"organization,":[31],"chromatin":[32],"remodeling":[33],"key":[36],"mechanism":[37],"to":[38,63,192],"increase":[39],"proteomic":[40],"diversity.":[41],"Thus,":[42],"accurate":[43],"information":[44],"on":[45,86,103],"such":[46],"sites":[47,68,102],"beneficial":[49],"for":[50,97,129],"both":[51],"drug":[52],"development":[53],"basic":[55],"research.":[56],"Existing":[57],"computational":[58],"methods":[59],"can":[60,185],"be":[61],"improved":[62],"more":[64],"effectively":[65],"identify":[66],"Kcr":[67,101],"In":[71],"this":[72],"study,":[73],"we":[74,172],"proposed":[75,110,135],"deep":[77],"learning":[78],"model,":[79],"DeepCap-Kcr,":[80],"capsule":[82,182],"network":[83,90],"(CapsNet)":[84],"based":[85],"convolutional":[88],"neural":[89],"(CNN)":[91],"long":[93],"short-term":[94],"memory":[95],"(LSTM)":[96],"robust":[98],"prediction":[99],"of":[100,151,159],"proteins":[107],"(mammals).":[108],"The":[109,161,199],"model":[111,136,163],"outperformed":[112],"the":[113,134,138,145,174,180,187],"existing":[114],"CNN":[115],"architecture":[116],"Deep-Kcr":[117],"other":[119,168],"well-established":[120],"tools":[121],"most":[123],"cases":[124],"provided":[126],"promising":[127],"outcomes":[128],"practical":[130],"use;":[131],"particular,":[133],"characterized":[137],"internal":[139,181,188],"hierarchical":[140],"representation":[141],"as":[142,144],"well":[143,165],"important":[146],"features":[147,175],"from":[148,155],"multiple":[149],"levels":[150],"abstraction":[152],"automatically":[153],"learned":[154],"small":[157],"number":[158],"samples.":[160],"trained":[162],"was":[164],"generalized":[166],"species":[169],"(papaya).":[170],"Moreover,":[171],"showed":[173],"properties":[177],"generated":[178],"by":[179],"layer":[183],"that":[184],"explore":[186],"data":[189,203],"distribution":[190],"related":[191],"biological":[193],"significance":[194],"(as":[195],"motif":[197],"detector).":[198],"source":[200],"code":[201],"are":[204],"freely":[205],"available":[206],"at":[207],"https://github.com/Jhabindra-bioinfo/DeepCap-Kcr.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":13}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
