{"id":"https://openalex.org/W2140735973","doi":"https://doi.org/10.1093/bioinformatics/btn037","title":"ConFunc\u2014functional annotation in the twilight zone","display_name":"ConFunc\u2014functional annotation in the twilight zone","publication_year":2008,"publication_date":"2008-02-08","ids":{"openalex":"https://openalex.org/W2140735973","doi":"https://doi.org/10.1093/bioinformatics/btn037","mag":"2140735973","pmid":"https://pubmed.ncbi.nlm.nih.gov/18263643"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn037","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn037","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btn037","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054810742","display_name":"Mark N. Wass","orcid":"https://orcid.org/0000-0001-5428-6479"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark N. Wass","raw_affiliation_strings":["Structural Bioinformatics Group, Biochemistry Building, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Structural Bioinformatics Group, Biochemistry Building, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023619547","display_name":"Michael J.E. Sternberg","orcid":"https://orcid.org/0000-0002-1884-5445"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Michael J. E. Sternberg","raw_affiliation_strings":["Structural Bioinformatics Group, Biochemistry Building, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Structural Bioinformatics Group, Biochemistry Building, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5023619547"],"corresponding_institution_ids":["https://openalex.org/I47508984"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":3.7671,"has_fulltext":false,"cited_by_count":106,"citation_normalized_percentile":{"value":0.9407812,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"24","issue":"6","first_page":"798","last_page":"806"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8418999910354614,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8418999910354614,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.062199998646974564,"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":0.049800001084804535,"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/annotation","display_name":"Annotation","score":0.7447099685668945},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5394691824913025},{"id":"https://openalex.org/keywords/twilight","display_name":"Twilight","score":0.5355201959609985},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2933192849159241}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7447099685668945},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5394691824913025},{"id":"https://openalex.org/C2777298776","wikidata":"https://www.wikidata.org/wiki/Q164160","display_name":"Twilight","level":2,"score":0.5355201959609985},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2933192849159241},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"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":"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"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":"D016415","descriptor_name":"Sequence Alignment","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},{"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":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btn037","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn037","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18263643","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18263643","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:kar.kent.ac.uk:31434","is_oa":false,"landing_page_url":"https://kar.kent.ac.uk/31434/","pdf_url":null,"source":{"id":"https://openalex.org/S4377196264","display_name":"Kent Academic Repository (University of Kent)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20581793","host_organization_name":"University of Kent","host_organization_lineage":["https://openalex.org/I20581793"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn037","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn037","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3352515238","display_name":null,"funder_award_id":"BB/D524508/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W21816278","https://openalex.org/W1538463803","https://openalex.org/W1964640688","https://openalex.org/W1964795578","https://openalex.org/W1965582988","https://openalex.org/W1976526581","https://openalex.org/W1986800180","https://openalex.org/W2003788979","https://openalex.org/W2032838501","https://openalex.org/W2051575557","https://openalex.org/W2055043387","https://openalex.org/W2059067075","https://openalex.org/W2064820767","https://openalex.org/W2068055268","https://openalex.org/W2068886104","https://openalex.org/W2083654996","https://openalex.org/W2084413241","https://openalex.org/W2097542211","https://openalex.org/W2100320834","https://openalex.org/W2101220662","https://openalex.org/W2103017472","https://openalex.org/W2103150692","https://openalex.org/W2106258670","https://openalex.org/W2114886480","https://openalex.org/W2115595474","https://openalex.org/W2119195082","https://openalex.org/W2121343862","https://openalex.org/W2123858481","https://openalex.org/W2124410686","https://openalex.org/W2127385662","https://openalex.org/W2127563440","https://openalex.org/W2132926880","https://openalex.org/W2135083016","https://openalex.org/W2136280642","https://openalex.org/W2137991504","https://openalex.org/W2139919097","https://openalex.org/W2143011057","https://openalex.org/W2143210482","https://openalex.org/W2150452501","https://openalex.org/W2158714788","https://openalex.org/W2160769697","https://openalex.org/W2161732286","https://openalex.org/W2167277498","https://openalex.org/W2167318540","https://openalex.org/W2799873608","https://openalex.org/W6641385041","https://openalex.org/W6682139550"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2341012202","https://openalex.org/W2329039841","https://openalex.org/W2606348389","https://openalex.org/W1621998790","https://openalex.org/W1824086156","https://openalex.org/W4320717050","https://openalex.org/W4241575677","https://openalex.org/W1653644159","https://openalex.org/W2949726873"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"success":[2],"of":[3,41,73,78,95,108,119,143,147,154,174],"genome":[4],"sequencing":[5],"has":[6],"resulted":[7],"in":[8,104],"many":[9],"protein":[10,23,86,102],"sequences":[11,42,144],"without":[12],"functional":[13],"annotation.":[14],"We":[15,91],"present":[16],"ConFunc,":[17,96],"an":[18,175],"automated":[19,176],"Gene":[20],"Ontology":[21],"(GO)-based":[22],"function":[24,87,103],"prediction":[25],"approach,":[26],"which":[27,63,85],"uses":[28],"conserved":[29],"residues":[30,54],"to":[31,35,49,100,171],"generate":[32],"sequence":[33,109,149],"profiles":[34,83],"infer":[36],"function.":[37],"ConFunc":[38,111,156,170],"split":[39],"sets":[40],"identified":[43,56],"by":[44,127],"PSI-BLAST":[45,99,116],"into":[46],"sub-alignments":[47],"according":[48],"their":[50],"GO":[51,59],"annotations.":[52],"Conserved":[53],"are":[55,124],"for":[57,62,138,169],"each":[58],"term":[60],"sub-alignment":[61],"a":[64,76,139],"position":[65],"specific":[66],"scoring":[67],"matrix":[68],"is":[69,88],"generated.":[70],"This":[71],"combination":[72],"steps":[74],"produces":[75],"set":[77,142],"feature":[79],"(GO":[80],"annotation)":[81],"derived":[82],"from":[84],"predicted.":[89],"RESULTS:":[90],"assess":[92],"the":[93,105,167],"ability":[94],"BLAST":[97,114],"and":[98,121,130],"predict":[101],"twilight":[106],"zone":[107],"similarity.":[110],"significantly":[112],"outperforms":[113],"&":[115],"obtaining":[117],"levels":[118,153],"recall":[120,158],"precision":[122,132],"that":[123],"not":[125],"obtained":[126],"either":[128],"method":[129],"maximum":[131],"24%":[133],"greater":[134,161],"than":[135,162],"BLAST.":[136,163],"Further":[137],"large":[140],"test":[141],"with":[145],"homologues":[146],"low":[148],"identity,":[150],"at":[151],"high":[152],"presicision,":[155],"obtains":[157],"six":[159],"times":[160],"These":[164],"results":[165],"demonstrate":[166],"potential":[168],"form":[172],"part":[173],"genomics":[177],"annotation":[178],"pipeline.":[179],"AVAILABILITY:":[180],"http://www.sbg.bio.ic.ac.uk/confunc":[181]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":11}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
