{"id":"https://openalex.org/W1988422871","doi":"https://doi.org/10.1093/nar/gki037","title":"3did: interacting protein domains of known three-dimensional structure","display_name":"3did: interacting protein domains of known three-dimensional structure","publication_year":2004,"publication_date":"2004-12-17","ids":{"openalex":"https://openalex.org/W1988422871","doi":"https://doi.org/10.1093/nar/gki037","mag":"1988422871","pmid":"https://pubmed.ncbi.nlm.nih.gov/15608228"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki037","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki037","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D413/7621683/gki037.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/D413/7621683/gki037.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032625918","display_name":"Amelie Stein","orcid":"https://orcid.org/0000-0002-5862-1681"},"institutions":[{"id":"https://openalex.org/I1303691731","display_name":"European Molecular Biology Organization","ror":"https://ror.org/04wfr2810","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I1303691731"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"A. Stein","raw_affiliation_strings":["EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany","EMBL, Meyerhofstrasse 1  69117 Heidelberg Germany"],"affiliations":[{"raw_affiliation_string":"EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I1303691731"]},{"raw_affiliation_string":"EMBL, Meyerhofstrasse 1  69117 Heidelberg Germany","institution_ids":["https://openalex.org/I1303691731"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5032625918"],"corresponding_institution_ids":["https://openalex.org/I1303691731"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":5.0647,"has_fulltext":true,"cited_by_count":181,"citation_normalized_percentile":{"value":0.96224315,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"Database issue","first_page":"D413","last_page":"D417"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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":0.9993000030517578,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9948999881744385,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10497","display_name":"Fungal and yeast genetics research","score":0.993399977684021,"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":0.7616344690322876},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.6444729566574097},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.5754474997520447},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5726791620254517},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5525991320610046},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.4887847602367401},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.4722194969654083},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4694606363773346},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.44166243076324463},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4151408076286316},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26583153009414673},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22716432809829712},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.22548088431358337}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7616344690322876},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.6444729566574097},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.5754474997520447},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5726791620254517},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5525991320610046},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.4887847602367401},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.4722194969654083},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4694606363773346},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.44166243076324463},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4151408076286316},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26583153009414673},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22716432809829712},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.22548088431358337},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","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}],"mesh":[{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","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":"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":5,"locations":[{"id":"doi:10.1093/nar/gki037","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki037","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D413/7621683/gki037.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:15608228","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15608228","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:10.1.1.977.3154","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.977.3154","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/content/33/suppl_1/D413.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:163496","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC539991","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:539991","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/539991","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/gki037","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki037","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D413/7621683/gki037.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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1988422871.pdf","grobid_xml":"https://content.openalex.org/works/W1988422871.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1988496202","https://openalex.org/W2026258231","https://openalex.org/W2037036397","https://openalex.org/W2039063819","https://openalex.org/W2040941311","https://openalex.org/W2065304353","https://openalex.org/W2083978969","https://openalex.org/W2084619201","https://openalex.org/W2099235960","https://openalex.org/W2103017472","https://openalex.org/W2104315543","https://openalex.org/W2113019448","https://openalex.org/W2113654464","https://openalex.org/W2124354935","https://openalex.org/W2125725297","https://openalex.org/W2128888818","https://openalex.org/W2140455347","https://openalex.org/W2141885858","https://openalex.org/W2158714788","https://openalex.org/W2167869241","https://openalex.org/W3095583226","https://openalex.org/W4210400672"],"related_works":["https://openalex.org/W2010825547","https://openalex.org/W2045131140","https://openalex.org/W2914490533","https://openalex.org/W2364094720","https://openalex.org/W2118652015","https://openalex.org/W1999731297","https://openalex.org/W2133671332","https://openalex.org/W2800194647","https://openalex.org/W2063692638","https://openalex.org/W853003716"],"abstract_inverted_index":{"The":[0,57],"database":[1,58],"of":[2,10,42,52],"3D":[3],"Interacting":[4],"Domains":[5],"(3did)":[6],"is":[7,81],"a":[8],"collection":[9],"domain-domain":[11],"interactions":[12,35,48,66],"in":[13,45],"proteins":[14,69],"for":[15,32],"which":[16],"high-resolution":[17],"three-dimensional":[18],"structures":[19],"are":[20,47],"known.":[21],"3did":[22,80],"exploits":[23],"structural":[24],"information":[25],"to":[26,78],"provide":[27],"critical":[28],"molecular":[29],"details":[30],"necessary":[31],"understanding":[33],"how":[34,43],"occur.":[36],"It":[37],"also":[38,59],"offers":[39],"an":[40],"overview":[41],"similar":[44],"structure":[46],"between":[49,67],"different":[50],"members":[51],"the":[53],"same":[54],"protein":[55],"family.":[56],"contains":[60],"Gene":[61],"Ontology-based":[62],"functional":[63],"annotations":[64],"and":[65],"yeast":[68],"from":[70],"large-scale":[71],"interaction":[72],"discovery":[73],"studies.":[74],"A":[75],"web-based":[76],"tool":[77],"query":[79],"available":[82],"at":[83],"http://3did.embl.de.":[84]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":14}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}