{"id":"https://openalex.org/W1968697272","doi":"https://doi.org/10.1093/nar/gki096","title":"ADDA: a domain database with global coverage of the protein universe","display_name":"ADDA: a domain database with global coverage of the protein universe","publication_year":2004,"publication_date":"2004-12-17","ids":{"openalex":"https://openalex.org/W1968697272","doi":"https://doi.org/10.1093/nar/gki096","mag":"1968697272","pmid":"https://pubmed.ncbi.nlm.nih.gov/15608174"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki096","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D188/7622193/gki096.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":"hybrid","oa_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D188/7622193/gki096.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021930729","display_name":"Andreas Heger","orcid":"https://orcid.org/0000-0001-7720-0447"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I2800229700","display_name":"Helsinki Institute of Physics","ror":"https://ror.org/01x2x1522","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I2800229700","https://openalex.org/I63548447","https://openalex.org/I94722563","https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"A. Heger","raw_affiliation_strings":["Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland. andreas.heger@helsinki.fi","Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland. andreas.heger@helsinki.fi","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I2800229700"]},{"raw_affiliation_string":"Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5021930729"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I2800229700"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.247,"has_fulltext":true,"cited_by_count":48,"citation_normalized_percentile":{"value":0.76246038,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"Database issue","first_page":"D188","last_page":"D191"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9988999962806702,"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":0.9988999962806702,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.998199999332428,"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/biology","display_name":"Biology","score":0.7459895610809326},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.7427560687065125},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6944758892059326},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.6939535737037659},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.6013357043266296},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4360891282558441},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.42331206798553467},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.41569453477859497},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3218100070953369},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2768182158470154},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2717185616493225},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.13032421469688416}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7459895610809326},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.7427560687065125},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6944758892059326},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.6939535737037659},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.6013357043266296},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4360891282558441},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.42331206798553467},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.41569453477859497},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3218100070953369},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2768182158470154},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2717185616493225},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.13032421469688416},{"id":"https://openalex.org/C55352822","wikidata":"https://www.wikidata.org/wiki/Q5558978","display_name":"Gibbs isotherm","level":3,"score":0.0},{"id":"https://openalex.org/C58226133","wikidata":"https://www.wikidata.org/wiki/Q1324199","display_name":"Pulmonary surfactant","level":2,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"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":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gki096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki096","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D188/7622193/gki096.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15608174","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15608174","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:CiteSeerX.psu:10.1.1.98.4881","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.98.4881","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/cgi/reprint/33/suppl_1/D188.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:163542","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC540050","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:540050","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/540050","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":"doi:10.1093/nar/gki096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki096","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D188/7622193/gki096.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1968697272.pdf","grobid_xml":"https://content.openalex.org/works/W1968697272.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W2007745123","https://openalex.org/W2026258231","https://openalex.org/W2046310275","https://openalex.org/W2050956531","https://openalex.org/W2087885007","https://openalex.org/W2108401170","https://openalex.org/W2122232025","https://openalex.org/W2125725297","https://openalex.org/W2126975650","https://openalex.org/W2130479394","https://openalex.org/W2140455347","https://openalex.org/W2141885858","https://openalex.org/W2154139219","https://openalex.org/W2155520400","https://openalex.org/W2158714788","https://openalex.org/W3095583226","https://openalex.org/W4210400672","https://openalex.org/W4241391257"],"related_works":["https://openalex.org/W2010825547","https://openalex.org/W2152281406","https://openalex.org/W1970034234","https://openalex.org/W2107811186","https://openalex.org/W2027811431","https://openalex.org/W1973695911","https://openalex.org/W1968697272","https://openalex.org/W2978954866","https://openalex.org/W1571895549","https://openalex.org/W2111805188"],"abstract_inverted_index":{"We":[0],"used":[1],"the":[2,71],"Automatic":[3],"Domain":[4],"Decomposition":[5],"Algorithm":[6],"(ADDA)":[7],"to":[8],"generate":[9],"a":[10,37,89],"database":[11,43],"of":[12,19],"protein":[13,21,33],"domain":[14,34,56,64,73],"families":[15,35,65],"with":[16,70],"complete":[17],"coverage":[18],"all":[20],"sequences.":[22],"Sequences":[23],"are":[24,30,61,81],"split":[25],"into":[26,32],"domains":[27,29,45],"and":[28,77,86],"grouped":[31],"in":[36,52],"completely":[38],"automated":[39],"process.":[40],"The":[41,79],"current":[42],"contains":[44],"for":[46,84],"more":[47,53],"than":[48,54],"1.5":[49],"million":[50],"sequences":[51],"40,000":[55],"families.":[57],"In":[58],"particular,":[59],"there":[60],"3828":[62],"novel":[63],"that":[66],"do":[67],"not":[68],"overlap":[69],"curated":[72],"databases":[74],"Pfam,":[75],"SCOP":[76],"InterPro.":[78],"data":[80],"freely":[82],"available":[83],"downloading":[85],"querying":[87],"via":[88],"web":[90],"interface":[91],"(http://ekhidna.biocenter.helsinki.fi:9801/sqgraph/pairsdb).":[92]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
