{"id":"https://openalex.org/W3027689783","doi":"https://doi.org/10.1093/bib/bbaa051","title":"PL-search: a profile-link-based search method for protein remote homology detection","display_name":"PL-search: a profile-link-based search method for protein remote homology detection","publication_year":2020,"publication_date":"2020-03-12","ids":{"openalex":"https://openalex.org/W3027689783","doi":"https://doi.org/10.1093/bib/bbaa051","mag":"3027689783","pmid":"https://pubmed.ncbi.nlm.nih.gov/32427287"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa051","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa051","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/A5035826694","display_name":"Xiaopeng Jin","orcid":"https://orcid.org/0000-0002-0058-8364"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Xiaopeng Jin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069241620","display_name":"Qing Liao","orcid":"https://orcid.org/0000-0003-1012-5301"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Qing Liao","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5100395591","display_name":"Bin Liu","orcid":"https://orcid.org/0000-0003-3685-9469"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bin Liu","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5035826694"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.7457,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.6887038,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"22","issue":"3","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":0.9984999895095825,"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":0.9937999844551086,"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":0.7233638763427734},{"id":"https://openalex.org/keywords/jaccard-index","display_name":"Jaccard index","score":0.6951860785484314},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.6108432412147522},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.5372820496559143},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.45524686574935913},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4464600682258606},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43076181411743164},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.43051135540008545},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.41841331124305725},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4140603244304657},{"id":"https://openalex.org/keywords/beam-search","display_name":"Beam search","score":0.41300472617149353},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.26625850796699524},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.22624695301055908}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7233638763427734},{"id":"https://openalex.org/C203519979","wikidata":"https://www.wikidata.org/wiki/Q865360","display_name":"Jaccard index","level":3,"score":0.6951860785484314},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.6108432412147522},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.5372820496559143},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.45524686574935913},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4464600682258606},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43076181411743164},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.43051135540008545},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.41841331124305725},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4140603244304657},{"id":"https://openalex.org/C19889080","wikidata":"https://www.wikidata.org/wiki/Q2835852","display_name":"Beam search","level":3,"score":0.41300472617149353},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.26625850796699524},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.22624695301055908},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa051","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa051","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:32427287","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32427287","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":[],"awards":[{"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/G6876496325","display_name":null,"funder_award_id":"JQ19019","funder_id":"https://openalex.org/F4320322919","funder_display_name":"Natural Science Foundation of Beijing Municipality"},{"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/F4320322919","display_name":"Natural Science Foundation of Beijing Municipality","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1558365920","https://openalex.org/W2047544230","https://openalex.org/W2051210555","https://openalex.org/W2062693912","https://openalex.org/W2069458148","https://openalex.org/W2084787613","https://openalex.org/W2086320398","https://openalex.org/W2087064593","https://openalex.org/W2094140553","https://openalex.org/W2095719242","https://openalex.org/W2096748155","https://openalex.org/W2098101556","https://openalex.org/W2110434201","https://openalex.org/W2133075481","https://openalex.org/W2133312664","https://openalex.org/W2135621733","https://openalex.org/W2138122982","https://openalex.org/W2138621811","https://openalex.org/W2139271731","https://openalex.org/W2139621307","https://openalex.org/W2144362290","https://openalex.org/W2145268834","https://openalex.org/W2145931647","https://openalex.org/W2157825442","https://openalex.org/W2157975034","https://openalex.org/W2158714788","https://openalex.org/W2293040502","https://openalex.org/W2302778906","https://openalex.org/W2343212594","https://openalex.org/W2550969987","https://openalex.org/W2560534849","https://openalex.org/W2575281222","https://openalex.org/W2584637367","https://openalex.org/W2606325896","https://openalex.org/W2735194059","https://openalex.org/W2786016794","https://openalex.org/W2887757903","https://openalex.org/W2902353954","https://openalex.org/W2911349016","https://openalex.org/W2963579612","https://openalex.org/W2979937512","https://openalex.org/W2981438385","https://openalex.org/W6758364508","https://openalex.org/W6929990038"],"related_works":["https://openalex.org/W4386269615","https://openalex.org/W4390091683","https://openalex.org/W1994919150","https://openalex.org/W58921990","https://openalex.org/W2204575588","https://openalex.org/W2081821176","https://openalex.org/W3106196307","https://openalex.org/W3084994579","https://openalex.org/W2998661990","https://openalex.org/W3115021520"],"abstract_inverted_index":{"Protein":[0],"remote":[1,29,112,154],"homology":[2],"detection":[3,25],"is":[4,104,134],"a":[5,77],"fundamental":[6],"and":[7,13,31,43,75,92,96,166],"important":[8],"task":[9],"for":[10,69,111],"protein":[11],"structure":[12],"function":[14],"analysis.":[15],"Several":[16],"search":[17,58,79,140],"methods":[18],"have":[19],"been":[20],"proposed":[21,76],"to":[22,51],"improve":[23],"the":[24,28,32,53,56,65,90,107,139,150,167],"performance":[26,54,141],"of":[27,34,55,101,144,152,158,160],"homologues":[30],"accuracy":[33],"ranking":[35,145],"lists.":[36],"The":[37],"position-specific":[38,132],"scoring":[39],"matrix":[40],"(PSSM)":[41],"profile":[42,48],"hidden":[44],"Markov":[45],"model":[46],"(HMM)":[47],"can":[49,173],"contribute":[50],"improving":[52],"state-of-the-art":[57],"methods.":[59],"In":[60,82],"this":[61],"paper,":[62],"we":[63],"improved":[64],"profile-link":[66],"(PL)":[67],"information":[68],"constructing":[70],"PSSM":[71],"or":[72,131],"HMM":[73],"profiles,":[74],"PL-based":[78],"method":[80,117],"(PL-search).":[81],"PL-search,":[83,161],"more":[84],"robust":[85],"PLs":[86],"are":[87,170],"constructed":[88],"through":[89],"double-link":[91],"iterative":[93],"extending":[94],"strategies,":[95],"an":[97],"accurate":[98],"similarity":[99],"score":[100],"sequence":[102],"pairs":[103],"calculated":[105],"from":[106],"two-level":[108],"Jaccard":[109],"distance":[110],"homologues.":[113,155],"We":[114],"tested":[115],"our":[116],"on":[118],"two":[119],"widely":[120],"used":[121],"benchmark":[122],"datasets.":[123],"Our":[124],"results":[125],"show":[126],"that":[127],"whether":[128],"HHblits,":[129],"JackHMMER":[130],"iterated-BLAST":[133],"used,":[135],"PL-search":[136],"obviously":[137],"improves":[138],"in":[142],"terms":[143],"quality":[146],"as":[147,149],"well":[148],"number":[151],"detected":[153],"For":[156],"ease":[157],"use":[159],"both":[162],"its":[163],"stand-alone":[164],"tool":[165],"web":[168],"server":[169],"constructed,":[171],"which":[172],"be":[174],"accessed":[175],"at":[176],"http://bliulab.net/PL-search/.":[177]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
