{"id":"https://openalex.org/W2550969987","doi":"https://doi.org/10.1093/bib/bbw108","title":"A comprehensive review and comparison of different computational methods for protein remote homology detection","display_name":"A comprehensive review and comparison of different computational methods for protein remote homology detection","publication_year":2016,"publication_date":"2016-10-24","ids":{"openalex":"https://openalex.org/W2550969987","doi":"https://doi.org/10.1093/bib/bbw108","mag":"2550969987","pmid":"https://pubmed.ncbi.nlm.nih.gov/27881430"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbw108","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbw108","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/A5100365536","display_name":"Junjie Chen","orcid":"https://orcid.org/0000-0002-0483-303X"},"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":"Junjie Chen","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006863868","display_name":"Mingyue Guo","orcid":"https://orcid.org/0000-0002-2202-157X"},"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":"Mingyue Guo","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100424254","display_name":"Xiaolong Wang","orcid":"https://orcid.org/0000-0001-9003-4252"},"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":"Xiaolong Wang","raw_affiliation_strings":["Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"last","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":["Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I204983213"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100395591"],"corresponding_institution_ids":["https://openalex.org/I204983213"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":9.2984,"has_fulltext":false,"cited_by_count":149,"citation_normalized_percentile":{"value":0.98445122,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"19","issue":"2","first_page":"231","last_page":"244"},"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":0.9980999827384949,"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":0.992900013923645,"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":0.7214657664299011},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.6814595460891724},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.49641066789627075},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.4866839051246643},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.4691148102283478},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4537232220172882},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.44835150241851807},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36617618799209595},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16865947842597961},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.09995490312576294},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07463860511779785},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.07150325179100037}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7214657664299011},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.6814595460891724},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.49641066789627075},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.4866839051246643},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.4691148102283478},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4537232220172882},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44835150241851807},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36617618799209595},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16865947842597961},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.09995490312576294},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07463860511779785},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.07150325179100037},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbw108","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbw108","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:27881430","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27881430","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":[{"score":0.7599999904632568,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G4554238193","display_name":null,"funder_award_id":"2014A030313695","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"},{"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"},{"id":"https://openalex.org/G8170964775","display_name":null,"funder_award_id":"61300112 and 61573118","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8428187204","display_name":null,"funder_award_id":"61672184, 61300112 and 61573118","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":123,"referenced_works":["https://openalex.org/W78256357","https://openalex.org/W1486662173","https://openalex.org/W1494484168","https://openalex.org/W1592614241","https://openalex.org/W1917981667","https://openalex.org/W1964145490","https://openalex.org/W1966191115","https://openalex.org/W1969051510","https://openalex.org/W1969478688","https://openalex.org/W1971650367","https://openalex.org/W1973714307","https://openalex.org/W1975394843","https://openalex.org/W1978201669","https://openalex.org/W1983320747","https://openalex.org/W1989443283","https://openalex.org/W1990446639","https://openalex.org/W1991910500","https://openalex.org/W2008907996","https://openalex.org/W2013788476","https://openalex.org/W2015292449","https://openalex.org/W2021312899","https://openalex.org/W2022247199","https://openalex.org/W2024503898","https://openalex.org/W2033855745","https://openalex.org/W2034115630","https://openalex.org/W2040644205","https://openalex.org/W2041840130","https://openalex.org/W2042507562","https://openalex.org/W2043338013","https://openalex.org/W2047444359","https://openalex.org/W2051210555","https://openalex.org/W2055043387","https://openalex.org/W2056499061","https://openalex.org/W2058071327","https://openalex.org/W2058833671","https://openalex.org/W2060145604","https://openalex.org/W2060259273","https://openalex.org/W2062693912","https://openalex.org/W2062760761","https://openalex.org/W2063389953","https://openalex.org/W2070980386","https://openalex.org/W2074231493","https://openalex.org/W2076048958","https://openalex.org/W2077514957","https://openalex.org/W2084787613","https://openalex.org/W2085140422","https://openalex.org/W2085277871","https://openalex.org/W2087064593","https://openalex.org/W2091374952","https://openalex.org/W2094764962","https://openalex.org/W2095692770","https://openalex.org/W2096041635","https://openalex.org/W2096748155","https://openalex.org/W2099182237","https://openalex.org/W2101220662","https://openalex.org/W2102122585","https://openalex.org/W2102652793","https://openalex.org/W2104873783","https://openalex.org/W2107539619","https://openalex.org/W2108067237","https://openalex.org/W2108079689","https://openalex.org/W2109806386","https://openalex.org/W2112815320","https://openalex.org/W2116977569","https://openalex.org/W2117502874","https://openalex.org/W2121950477","https://openalex.org/W2123525093","https://openalex.org/W2125725297","https://openalex.org/W2131889225","https://openalex.org/W2132122858","https://openalex.org/W2132402247","https://openalex.org/W2133075481","https://openalex.org/W2135621733","https://openalex.org/W2137193141","https://openalex.org/W2139621307","https://openalex.org/W2141885858","https://openalex.org/W2142013909","https://openalex.org/W2145268834","https://openalex.org/W2145957695","https://openalex.org/W2146084306","https://openalex.org/W2146442590","https://openalex.org/W2146628513","https://openalex.org/W2147660582","https://openalex.org/W2148279834","https://openalex.org/W2148603752","https://openalex.org/W2150248355","https://openalex.org/W2151180344","https://openalex.org/W2151831732","https://openalex.org/W2152311353","https://openalex.org/W2153153865","https://openalex.org/W2153720577","https://openalex.org/W2154218709","https://openalex.org/W2155744824","https://openalex.org/W2155792813","https://openalex.org/W2156125289","https://openalex.org/W2156226201","https://openalex.org/W2157122545","https://openalex.org/W2158714788","https://openalex.org/W2159590158","https://openalex.org/W2160865839","https://openalex.org/W2161072217","https://openalex.org/W2161710599","https://openalex.org/W2161943425","https://openalex.org/W2164949947","https://openalex.org/W2167785149","https://openalex.org/W2169079604","https://openalex.org/W2170960297","https://openalex.org/W2224056471","https://openalex.org/W2283504545","https://openalex.org/W2336842442","https://openalex.org/W2337731955","https://openalex.org/W2346963783","https://openalex.org/W2396235019","https://openalex.org/W2396236058","https://openalex.org/W2407836068","https://openalex.org/W2428387384","https://openalex.org/W2597289420","https://openalex.org/W2612240612","https://openalex.org/W2765779130","https://openalex.org/W2914238450","https://openalex.org/W3148081761","https://openalex.org/W4210400672","https://openalex.org/W6704973214"],"related_works":["https://openalex.org/W2965546495","https://openalex.org/W4389116644","https://openalex.org/W2153315159","https://openalex.org/W3103844505","https://openalex.org/W259157601","https://openalex.org/W4205463238","https://openalex.org/W2761785940","https://openalex.org/W2378211422","https://openalex.org/W2110523656","https://openalex.org/W1482209366"],"abstract_inverted_index":{"Protein":[0],"remote":[1,57],"homology":[2,58],"detection":[3],"is":[4,62,107],"one":[5],"of":[6,16],"the":[7,14,24,34],"most":[8],"fundamental":[9],"and":[10,19,69,91,96,104,125],"central":[11],"problems":[12],"for":[13],"studies":[15],"protein":[17,56],"structures":[18],"functions,":[20],"aiming":[21],"to":[22,43,55,64],"detect":[23],"distantly":[25],"evolutionary":[26],"relationships":[27],"among":[28],"proteins":[29],"via":[30],"computational":[31,38,73,81],"methods.":[32,74,93],"During":[33],"past":[35],"decades,":[36],"many":[37],"approaches":[39,82],"have":[40,50],"been":[41],"proposed":[42],"solve":[44],"this":[45,76,120],"important":[46],"task.":[47],"These":[48],"methods":[49,90],"made":[51],"a":[52,66,101],"substantial":[53],"contribution":[54],"detection.":[59],"Therefore,":[60],"it":[61],"necessary":[63],"give":[65],"comprehensive":[67,102],"review":[68],"comparison":[70],"on":[71,109],"these":[72,80],"In":[75],"article,":[77],"we":[78],"divide":[79],"into":[83],"three":[84],"categories,":[85],"including":[86],"alignment":[87],"methods,":[88],"discriminative":[89],"ranking":[92],"Their":[94],"advantages":[95],"disadvantages":[97],"are":[98,122],"discussed":[99],"in":[100,119],"perspective,":[103],"their":[105],"performance":[106],"compared":[108],"widely":[110],"used":[111],"benchmark":[112],"data":[113],"sets.":[114],"Finally,":[115],"some":[116],"open":[117],"questions":[118],"field":[121],"further":[123],"explored":[124],"discussed.":[126]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":30},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":16}],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2025-10-10T00:00:00"}
