{"id":"https://openalex.org/W4281257916","doi":"https://doi.org/10.1109/tcbb.2022.3175905","title":"DomBpred: Protein Domain Boundary Prediction Based on Domain-Residue Clustering Using Inter-Residue Distance","display_name":"DomBpred: Protein Domain Boundary Prediction Based on Domain-Residue Clustering Using Inter-Residue Distance","publication_year":2022,"publication_date":"2022-05-20","ids":{"openalex":"https://openalex.org/W4281257916","doi":"https://doi.org/10.1109/tcbb.2022.3175905","pmid":"https://pubmed.ncbi.nlm.nih.gov/35594218"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3175905","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3175905","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5029880532","display_name":"Zhong-Ze Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhong-Ze Yu","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061624407","display_name":"Chunxiang Peng","orcid":"https://orcid.org/0009-0006-9735-0278"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chun-Xiang Peng","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086734382","display_name":"Jun Liu","orcid":"https://orcid.org/0000-0002-8589-5514"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Liu","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100363712","display_name":"Biao Zhang","orcid":"https://orcid.org/0000-0001-8334-5175"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Biao Zhang","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023785113","display_name":"Xiaogen Zhou","orcid":"https://orcid.org/0000-0001-6839-1923"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao-Gen Zhou","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049735973","display_name":"Guijun Zhang","orcid":"https://orcid.org/0000-0002-7815-5884"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gui-Jun Zhang","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou, China"],"raw_orcid":"https://orcid.org/0000-0002-7815-5884","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou, China","institution_ids":["https://openalex.org/I55712492"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I55712492"],"apc_list":null,"apc_paid":null,"fwci":0.5876,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.62557103,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"20","issue":"2","first_page":"912","last_page":"922"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and 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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and 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"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9988999962806702,"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":0.989799976348877,"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/residue","display_name":"Residue (chemistry)","score":0.8340126276016235},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5867233276367188},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.47175177931785583},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.348200261592865},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2998943328857422},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2854832410812378},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2052733600139618},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.09138011932373047},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06249678134918213}],"concepts":[{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.8340126276016235},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5867233276367188},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.47175177931785583},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.348200261592865},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2998943328857422},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2854832410812378},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2052733600139618},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.09138011932373047},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06249678134918213}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2022.3175905","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3175905","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35594218","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35594218","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2708836668","display_name":null,"funder_award_id":"61773346","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3775454306","display_name":null,"funder_award_id":"62173304","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1979132333","https://openalex.org/W1996150123","https://openalex.org/W2037312364","https://openalex.org/W2069458148","https://openalex.org/W2078247418","https://openalex.org/W2092182190","https://openalex.org/W2119542589","https://openalex.org/W2119902292","https://openalex.org/W2126677834","https://openalex.org/W2129834345","https://openalex.org/W2130647858","https://openalex.org/W2137736270","https://openalex.org/W2138116388","https://openalex.org/W2147805410","https://openalex.org/W2153187042","https://openalex.org/W2160649303","https://openalex.org/W2170449429","https://openalex.org/W2579272540","https://openalex.org/W2613997260","https://openalex.org/W2899664253","https://openalex.org/W2902353954","https://openalex.org/W2903445992","https://openalex.org/W2949867299","https://openalex.org/W2952126842","https://openalex.org/W2963436022","https://openalex.org/W2997234557","https://openalex.org/W2999044305","https://openalex.org/W3014088204","https://openalex.org/W3106745904","https://openalex.org/W3127535326","https://openalex.org/W3164566829","https://openalex.org/W3177828909","https://openalex.org/W4253476860","https://openalex.org/W4285816840","https://openalex.org/W4320301318"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Domain":[0],"boundary":[1,26,48,132,199],"prediction":[2,27],"is":[3,57,94,135,150,190,257],"one":[4],"of":[5,13,114,157,206,221],"the":[6,11,54,83,98,109,112,115,121,140,146,170,186,197,222,232,250,263],"most":[7,24,240],"important":[8],"problems":[9],"in":[10,34,173],"study":[12],"protein":[14,46,64,68,176],"structure":[15,123],"and":[16,32,108,185,201,210,216,244,262],"function,":[17],"especially":[18],"for":[19],"large":[20],"proteins.":[21,38,161],"At":[22],"present,":[23],"domain":[25,47,131,147,198,203],"methods":[28,172,230,243],"have":[29],"low":[30],"accuracy":[31],"limitations":[33],"dealing":[35],"with":[36,228],"multi-domain":[37,67,84,195],"In":[39,52],"this":[40],"study,":[41],"we":[42],"develop":[43],"a":[44,62,66,70,77,86,130,153],"sequence-based":[45,242],"prediction,":[49],"named":[50],"DomBpred.":[51],"DomBpred,":[53],"input":[55],"sequence":[56,73,80],"first":[58],"classified":[59],"as":[60],"either":[61],"single-domain":[63,79],"or":[65,182],"through":[69],"designed":[71],"effective":[72],"metric":[74],"based":[75],"on":[76,152,193,231],"constructed":[78],"library.":[81],"For":[82],"protein,":[85],"domain-residue":[87],"clustering":[88],"algorithm":[89],"inspired":[90],"by":[91,120,180],"Ising":[92],"model":[93],"proposed":[95,136],"to":[96,124,137,144],"cluster":[97,116],"spatially":[99],"close":[100],"residues":[101,107,110],"according":[102],"inter-residue":[103],"distance.":[104],"The":[105,254],"unclassified":[106],"at":[111,260,266],"edge":[113],"are":[117,178,208,214],"then":[118],"tuned":[119],"secondary":[122],"form":[125],"potential":[126,141],"cut":[127,142],"points.":[128],"Finally,":[129],"scoring":[133],"function":[134],"recursively":[138],"evaluate":[139],"points":[143],"generate":[145],"boundary.":[148],"DomBpred":[149,166,207,238],"tested":[151],"large-scale":[154],"test":[155,234],"set":[156,235],"FUpred":[158],"comprising":[159],"2549":[160],"Experimental":[162],"results":[163,248],"show":[164],"that":[165,237],"better":[167,247],"performs":[168],"than":[169,219,249],"state-of-the-art":[171,241],"classifying":[174],"whether":[175],"sequences":[177],"composed":[179],"single":[181],"multiple":[183],"domains,":[184],"Matthew's":[187],"correlation":[188],"coefficient":[189],"0.882.":[191],"Moreover,":[192],"849":[194],"proteins,":[196],"distance":[200],"normalised":[202],"overlap":[204],"scores":[205],"0.523":[209],"0.824,":[211],"respectively,":[212],"which":[213],"5.0%":[215],"4.2%":[217],"higher":[218],"those":[220],"best":[223],"comparison":[224],"method,":[225],"respectively.":[226],"Comparison":[227],"other":[229],"given":[233],"shows":[236],"outperforms":[239],"even":[245],"achieves":[246],"top-level":[251],"template-based":[252],"method.":[253],"executable":[255],"program":[256],"freely":[258],"available":[259],"https://github.com/iobio-zjut/DomBpred":[261],"online":[264],"server":[265],"http://zhanglab-bioinf.com/DomBpred/.":[267]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
