{"id":"https://openalex.org/W2911349016","doi":"https://doi.org/10.1093/bib/bby104","title":"HITS-PR-HHblits: protein remote homology detection by combining PageRank and Hyperlink-Induced Topic Search","display_name":"HITS-PR-HHblits: protein remote homology detection by combining PageRank and Hyperlink-Induced Topic Search","publication_year":2018,"publication_date":"2018-10-05","ids":{"openalex":"https://openalex.org/W2911349016","doi":"https://doi.org/10.1093/bib/bby104","mag":"2911349016","pmid":"https://pubmed.ncbi.nlm.nih.gov/30403770"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby104","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby104","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/A5100395591","display_name":"Bin Liu","orcid":"https://orcid.org/0000-0003-3685-9469"},"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":"Bin Liu","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110850247","display_name":"Shuangyan Jiang","orcid":null},"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":"Shuangyan Jiang","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"last","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, China"],"affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China","institution_ids":["https://openalex.org/I150229711"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5017426085","https://openalex.org/A5100395591"],"corresponding_institution_ids":["https://openalex.org/I150229711","https://openalex.org/I204983213"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":5.1476,"has_fulltext":false,"cited_by_count":81,"citation_normalized_percentile":{"value":0.9658561,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"21","issue":"1","first_page":"298","last_page":"308"},"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":0.9975000023841858,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9767000079154968,"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":0.7895561456680298},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6230113506317139},{"id":"https://openalex.org/keywords/hyperlink","display_name":"Hyperlink","score":0.6200376152992249},{"id":"https://openalex.org/keywords/pagerank","display_name":"PageRank","score":0.5199224352836609},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.48102623224258423},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.4711821377277374},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.439973384141922},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.4190228581428528},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.18932005763053894},{"id":"https://openalex.org/keywords/web-page","display_name":"Web page","score":0.17803797125816345},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1691567301750183},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1644211709499359},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09303632378578186}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7895561456680298},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6230113506317139},{"id":"https://openalex.org/C30088001","wikidata":"https://www.wikidata.org/wiki/Q102014","display_name":"Hyperlink","level":3,"score":0.6200376152992249},{"id":"https://openalex.org/C2779172887","wikidata":"https://www.wikidata.org/wiki/Q184316","display_name":"PageRank","level":2,"score":0.5199224352836609},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.48102623224258423},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.4711821377277374},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.439973384141922},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.4190228581428528},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.18932005763053894},{"id":"https://openalex.org/C21959979","wikidata":"https://www.wikidata.org/wiki/Q36774","display_name":"Web page","level":2,"score":0.17803797125816345},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1691567301750183},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1644211709499359},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09303632378578186},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bby104","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby104","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:30403770","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30403770","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":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G1587116901","display_name":null,"funder_award_id":"61771331","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4864480503","display_name":null,"funder_award_id":"61822306","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5119273177","display_name":null,"funder_award_id":"2016A030306008","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"},{"id":"https://openalex.org/G74711194","display_name":null,"funder_award_id":"61732012","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G75457812","display_name":null,"funder_award_id":"61672184","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"},{"id":"https://openalex.org/F4320321921","display_name":"Natural Science Foundation of Guangdong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1494484168","https://openalex.org/W1517955486","https://openalex.org/W1803102843","https://openalex.org/W1973714307","https://openalex.org/W2015530520","https://openalex.org/W2034115630","https://openalex.org/W2039302875","https://openalex.org/W2042507562","https://openalex.org/W2051210555","https://openalex.org/W2055043387","https://openalex.org/W2058833671","https://openalex.org/W2062296203","https://openalex.org/W2070980386","https://openalex.org/W2080336769","https://openalex.org/W2080432979","https://openalex.org/W2084787613","https://openalex.org/W2089499735","https://openalex.org/W2090123586","https://openalex.org/W2091374952","https://openalex.org/W2094140553","https://openalex.org/W2096748155","https://openalex.org/W2097632784","https://openalex.org/W2100301244","https://openalex.org/W2117502874","https://openalex.org/W2117897510","https://openalex.org/W2120401481","https://openalex.org/W2121950477","https://openalex.org/W2122090784","https://openalex.org/W2124181495","https://openalex.org/W2132402247","https://openalex.org/W2133075481","https://openalex.org/W2135621733","https://openalex.org/W2137775453","https://openalex.org/W2138621811","https://openalex.org/W2139621307","https://openalex.org/W2146628513","https://openalex.org/W2147660582","https://openalex.org/W2148834305","https://openalex.org/W2150248355","https://openalex.org/W2153720577","https://openalex.org/W2157825442","https://openalex.org/W2158714788","https://openalex.org/W2283504545","https://openalex.org/W2344144945","https://openalex.org/W2436244623","https://openalex.org/W2510820101","https://openalex.org/W2550969987","https://openalex.org/W2570408261","https://openalex.org/W2571299862","https://openalex.org/W2726870159","https://openalex.org/W2761495217","https://openalex.org/W2780936345","https://openalex.org/W2782148675","https://openalex.org/W2793168264","https://openalex.org/W3026721701","https://openalex.org/W6667898854","https://openalex.org/W6729993066","https://openalex.org/W6747408139","https://openalex.org/W6747693122"],"related_works":["https://openalex.org/W4248250357","https://openalex.org/W2140393699","https://openalex.org/W2150410176","https://openalex.org/W2351647974","https://openalex.org/W2542162642","https://openalex.org/W1558012608","https://openalex.org/W2139195016","https://openalex.org/W2378303769","https://openalex.org/W1986226901","https://openalex.org/W2971959138"],"abstract_inverted_index":{"As":[0],"one":[1],"of":[2,95,145,151,201,247],"the":[3,61,73,78,92,98,101,108,112,142,149,152,156,175,180,186,191,199,202,217,222,225,230],"most":[4,203],"important":[5],"fundamental":[6],"problems":[7],"in":[8,81,97,155],"protein":[9,12,51,85,240],"sequence":[10],"analysis,":[11],"remote":[13,52,241],"homology":[14,53,242],"detection":[15,41,54,243],"is":[16,43,70,236],"critical":[17],"for":[18,209,239,257],"both":[19],"theoretical":[20],"research":[21],"(protein":[22],"structure":[23],"and":[24,27,67,100,123,128,160,165,182],"function":[25],"studies)":[26],"real":[28],"world":[29],"applications":[30],"(drug":[31],"design).":[32],"Although":[33],"several":[34],"computational":[35,255],"predictors":[36],"have":[37],"been":[38],"proposed,":[39],"their":[40],"performance":[42],"still":[44],"limited.":[45],"In":[46],"this":[47,138],"study,":[48],"we":[49],"treat":[50],"as":[55,65],"a":[56,82,166,206,237,252],"document":[57],"retrieval":[58],"task,":[59],"where":[60],"proteins":[62,96,103,144,147,154],"are":[63],"considered":[64],"documents":[66,76,80],"its":[68],"aim":[69],"to":[71,140,148,172,227],"find":[72],"highly":[74],"related":[75],"with":[77],"query":[79,102,146,153],"database.":[83],"A":[84],"similarity":[86,113],"network":[87,109,139],"was":[88,170,211],"constructed":[89],"based":[90,110],"on":[91,111,137,179],"true":[93],"labels":[94],"database,":[99],"were":[104,134,163],"then":[105],"connected":[106],"into":[107],"scores":[114],"calculated":[115],"by":[116,215],"three":[117],"ranking":[118],"methods,":[119],"including":[120],"PSI-BLAST,":[121],"Hmmer":[122],"HHblits.":[124],"The":[125,233],"PageRank":[126,159],"algorithm":[127,133],"Hyperlink-Induced":[129],"Topic":[130],"Search":[131],"(HITS)":[132],"respectively":[135],"performed":[136],"move":[141],"homologous":[143],"neighbors":[150],"network.":[157],"Finally,":[158],"HITS":[161],"algorithms":[162],"combined,":[164],"predictor":[167,235],"called":[168],"HITS-PR-HHblits":[169,210,234],"proposed":[171,192],"further":[173],"improve":[174],"predictive":[176],"performance.":[177],"Tested":[178],"SCOP":[181],"SCOPe":[183],"benchmark":[184],"datasets,":[185],"experimental":[187,204],"results":[188,223],"showed":[189],"that":[190],"protocols":[193],"outperformed":[194],"other":[195],"state-of-the-art":[196],"methods.":[197],"For":[198],"convenience":[200],"scientists,":[205],"web":[207],"server":[208],"established":[212],"at":[213],"http://bioinformatics.hitsz.edu.cn/HITS-PR-HHblits,":[214],"which":[216,249],"users":[218],"can":[219],"easily":[220],"get":[221],"without":[224],"need":[226],"go":[228],"through":[229],"mathematical":[231],"details.":[232],"protocol":[238],"using":[244],"different":[245],"sets":[246],"programs,":[248],"will":[250],"become":[251],"very":[253],"useful":[254],"tool":[256],"proteome":[258],"analysis.":[259]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":19},{"year":2019,"cited_by_count":22},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
