{"id":"https://openalex.org/W1996952741","doi":"https://doi.org/10.1093/nar/gkg051","title":"Gene3D: structural assignments for the biologist and bioinformaticist alike","display_name":"Gene3D: structural assignments for the biologist and bioinformaticist alike","publication_year":2003,"publication_date":"2003-01-01","ids":{"openalex":"https://openalex.org/W1996952741","doi":"https://doi.org/10.1093/nar/gkg051","mag":"1996952741","pmid":"https://pubmed.ncbi.nlm.nih.gov/12520054"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkg051","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar/gkg051","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":null,"any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087098726","display_name":"Daniel Buchan","orcid":"https://orcid.org/0000-0001-7391-4696"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"D. W. A. Buchan","raw_affiliation_strings":["Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK","Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5087098726"],"corresponding_institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":2.0593,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.8629544,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"31","issue":"1","first_page":"469","last_page":"473"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9966999888420105,"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":0.9957000017166138,"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/genome","display_name":"Genome","score":0.699063241481781},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6950126886367798},{"id":"https://openalex.org/keywords/file-transfer-protocol","display_name":"File Transfer Protocol","score":0.5777447819709778},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5192084908485413},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4727878272533417},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4191593527793884},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.40328294038772583},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.35874855518341064},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35344237089157104},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.33354049921035767},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.13844212889671326}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.699063241481781},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6950126886367798},{"id":"https://openalex.org/C169485995","wikidata":"https://www.wikidata.org/wiki/Q42283","display_name":"File Transfer Protocol","level":3,"score":0.5777447819709778},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5192084908485413},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4727878272533417},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4191593527793884},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.40328294038772583},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.35874855518341064},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35344237089157104},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33354049921035767},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.13844212889671326},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/nar/gkg051","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar/gkg051","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12520054","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12520054","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1298893","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/1298893/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"NUCLEIC ACIDS RES , 31 (1) 469 - 473. (2003)","raw_type":"Article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:53313","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/53313/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res , 31 (1) pp. 469-473. (2003)","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:158681","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC165498","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:165498","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:165498","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/165498","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:165498","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4300000071525574}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1513621883","https://openalex.org/W1585634379","https://openalex.org/W1839423960","https://openalex.org/W1982881067","https://openalex.org/W2003788979","https://openalex.org/W2009968404","https://openalex.org/W2018686514","https://openalex.org/W2095515048","https://openalex.org/W2099831744","https://openalex.org/W2109946226","https://openalex.org/W2110120447","https://openalex.org/W2115138247","https://openalex.org/W2122019155","https://openalex.org/W2124953719","https://openalex.org/W2140000393","https://openalex.org/W2141885858","https://openalex.org/W2142068542","https://openalex.org/W2142628689","https://openalex.org/W2147809382","https://openalex.org/W2155480785","https://openalex.org/W2158714788","https://openalex.org/W4210531204"],"related_works":["https://openalex.org/W2349516242","https://openalex.org/W2378353542","https://openalex.org/W2358003099","https://openalex.org/W2373243130","https://openalex.org/W2479761186","https://openalex.org/W3088189910","https://openalex.org/W2069131781","https://openalex.org/W646151359","https://openalex.org/W625983845","https://openalex.org/W623643430"],"abstract_inverted_index":{"The":[0,38],"Gene3D":[1,67,92,148],"database":[2,82,154],"(http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/)":[3],"provides":[4],"structural":[5,51,76,104,129,146],"assignments":[6,52,69,105],"for":[7,46,109],"genes":[8,126,142],"within":[9],"complete":[10],"genomes.":[11],"These":[12],"are":[13,27,62,131,143],"available":[14],"via":[15],"the":[16,20,35,48,84,137,141,152],"internet":[17],"from":[18],"either":[19],"World":[21],"Wide":[22],"Web":[23],"or":[24],"FTP.":[25],"Assignments":[26],"made":[28,53,65,108],"using":[29,34,54],"PSI-BLAST":[30],"and":[31,64,77,83,100,112,136,155],"subsequently":[32],"processed":[33],"DRange":[36,39],"protocol.":[37],"protocol":[40],"is":[41,149,156],"an":[42],"empirically":[43],"benchmarked":[44],"method":[45],"assessing":[47],"validity":[49],"of":[50,86,91,115,124,140,162],"sequence":[55],"searching":[56],"methods":[57],"where":[58],"appropriate":[59,72],"assignment":[60],"statistics":[61],"collected":[63],"available.":[66],"links":[68],"to":[70,151],"their":[71],"entries":[73],"in":[74],"relevent":[75],"classification":[78],"resources":[79],"(PDBsum,":[80],"CATH":[81,153],"Dictionary":[85],"Homologous":[87],"Superfamilies).":[88],"Release":[89],"2.0":[90],"includes":[93],"62":[94],"genomes,":[95],"2":[96],"eukaryotes,":[97],"10":[98],"archaea":[99],"40":[101,113],"bacteria.":[102],"Currently,":[103],"can":[106],"be":[107],"between":[110],"30":[111],"percent":[114],"any":[116,120],"given":[117],"genome.":[118],"In":[119],"genome,":[121],"around":[122],"half":[123,139],"those":[125],"assigned":[127,132,144],"a":[128,133],"domain":[130,135],"single":[134],"other":[138],"multiple":[145],"domains.":[147],"linked":[150],"updated":[157],"with":[158],"each":[159],"new":[160],"update":[161],"CATH.":[163]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
