{"id":"https://openalex.org/W2153261638","doi":"https://doi.org/10.1093/nar/gkj163","title":"E-MSD: improving data deposition and structure quality","display_name":"E-MSD: improving data deposition and structure quality","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W2153261638","doi":"https://doi.org/10.1093/nar/gkj163","mag":"2153261638","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381867"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj163","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj163","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D287/3926636/gkj163.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":true,"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":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D287/3926636/gkj163.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018343124","display_name":"M. Tagari","orcid":null},"institutions":[{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"funder","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"M. Tagari","raw_affiliation_strings":["Macromolecular Structure Database, EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","Macromolecular Structure Database, EMBL Outstation, European Bioinformatics Institute  Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"Macromolecular Structure Database, EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":[]},{"raw_affiliation_string":"Macromolecular Structure Database, EMBL Outstation, European Bioinformatics Institute  Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5018343124"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.8399,"has_fulltext":true,"cited_by_count":39,"citation_normalized_percentile":{"value":0.90926998,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"34","issue":"90001","first_page":"D287","last_page":"D290"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9894000291824341,"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":0.9839000105857849,"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/protein-data-bank","display_name":"Protein Data Bank","score":0.672997772693634},{"id":"https://openalex.org/keywords/data-quality","display_name":"Data quality","score":0.5608742237091064},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.508447527885437},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4784581661224365},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4081254005432129},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35535120964050293},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3221295475959778},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.20046424865722656},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11275014281272888},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.10092636942863464}],"concepts":[{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.672997772693634},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.5608742237091064},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.508447527885437},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4784581661224365},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4081254005432129},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35535120964050293},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3221295475959778},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.20046424865722656},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11275014281272888},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.10092636942863464},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005060","descriptor_name":"Europe","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005060","descriptor_name":"Europe","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005060","descriptor_name":"Europe","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008854","descriptor_name":"Microscopy, Electron","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008854","descriptor_name":"Microscopy, Electron","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008854","descriptor_name":"Microscopy, Electron","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","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":"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019906","descriptor_name":"Nuclear Magnetic Resonance, Biomolecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019906","descriptor_name":"Nuclear Magnetic Resonance, Biomolecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019906","descriptor_name":"Nuclear Magnetic Resonance, Biomolecular","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":"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},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkj163","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj163","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D287/3926636/gkj163.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":true,"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:16381867","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381867","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:pubmedcentral.nih.gov:1347525","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347525","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/gkj163","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj163","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D287/3926636/gkj163.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":true,"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":[{"id":"https://metadata.un.org/sdg/9","score":0.5299999713897705,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1990576317","display_name":null,"funder_award_id":"BBSRC","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2153261638.pdf","grobid_xml":"https://content.openalex.org/works/W2153261638.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1488741662","https://openalex.org/W1969983512","https://openalex.org/W1977845138","https://openalex.org/W1980824899","https://openalex.org/W2001641653","https://openalex.org/W2008519111","https://openalex.org/W2009517804","https://openalex.org/W2016255772","https://openalex.org/W2036348412","https://openalex.org/W2053158671","https://openalex.org/W2054591207","https://openalex.org/W2070876090","https://openalex.org/W2101648527","https://openalex.org/W2108401170","https://openalex.org/W2108491719","https://openalex.org/W2121002144","https://openalex.org/W2131639373","https://openalex.org/W2144998676","https://openalex.org/W2154139219","https://openalex.org/W2165739018","https://openalex.org/W2169707043","https://openalex.org/W2170338669","https://openalex.org/W4249030130"],"related_works":["https://openalex.org/W2020669016","https://openalex.org/W2088162897","https://openalex.org/W1488329660","https://openalex.org/W27170867","https://openalex.org/W2137479650","https://openalex.org/W2245479382","https://openalex.org/W3139296374","https://openalex.org/W4387803644","https://openalex.org/W4210350690","https://openalex.org/W2791222374"],"abstract_inverted_index":{"The":[0,126,163,185],"Macromolecular":[1,35],"Structure":[2,36],"Database":[3],"(MSD)":[4],"(http://www.ebi.ac.uk/msd/)":[5],"[H.":[6,73],"Boutselakis,":[7],"D.":[8],"Dimitropoulos,":[9],"J.":[10,18],"Fillon,":[11],"A.":[12,16,23],"Golovin,":[13],"K.":[14,75],"Henrick,":[15],"Hussain,":[17],"Ionides,":[19],"M.":[20],"John,":[21],"P.":[22],"Keller,":[24],"E.":[25],"Krissinel":[26],"et":[27],"al.":[28],"(2003)":[29,80],"E-MSD:":[30],"the":[31,47,51,56,60,66,82,95,103,107,123,132,140,148,158,161,170,175,181,188,193,213,219,227,232,237],"European":[32],"Bioinformatics":[33],"Institute":[34],"Database.":[37],"Nucleic":[38],"Acids":[39],"Res.,":[40],"31,":[41],"458-462.]":[42],"group":[43,97],"is":[44],"one":[45],"of":[46,65,69,109,142,150,157,177,187,196,215,239],"three":[48,164],"partners":[49,101,165],"in":[50,122,128,131,147,160,212,226],"worldwide":[52,83],"Protein":[53,84],"DataBank":[54],"(wwPDB),":[55],"consortium":[57],"entrusted":[58],"with":[59,100,192],"collation,":[61],"maintenance":[62],"and":[63,77,120,172,199,205,223,229],"distribution":[64],"global":[67],"repository":[68],"macromolecular":[70],"structure":[71],"data":[72,129,145,159,179,202,216],"Berman,":[74],"Henrick":[76],"H.":[78],"Nakamura":[79],"Announcing":[81],"Data":[85],"Bank.":[86],"Nature":[87],"Struct.":[88],"Biol.,":[89],"10,":[90],"980.].":[91],"Since":[92],"its":[93],"inception,":[94],"MSD":[96,189,233],"has":[98,207],"worked":[99],"around":[102],"world":[104],"to":[105,209,235],"improve":[106,236],"quality":[108,130,214,238],"PDB":[110],"data,":[111],"through":[112,139],"a":[113,143,151],"clean":[114],"up":[115],"programme":[116],"that":[117,154,217],"addresses":[118],"inconsistencies":[119],"inaccuracies":[121],"legacy":[124,133],"archive.":[125,220],"improvements":[127,211],"archive":[134],"have":[135],"been":[136],"achieved":[137],"largely":[138],"creation":[141],"unified":[144],"archive,":[146],"form":[149],"relational":[152],"database":[153],"stores":[155],"all":[156],"wwPDB.":[162],"are":[166],"working":[167],"towards":[168],"improving":[169],"tools":[171,198],"methods":[173],"for":[174,201],"deposition":[176],"new":[178],"by":[180],"community":[182],"at":[183],"large.":[184],"implementation":[186],"database,":[190],"together":[191],"parallel":[194],"development":[195],"improved":[197],"methodologies":[200],"harvesting,":[203],"validation":[204],"archival,":[206],"lead":[208],"significant":[210],"enters":[218],"Through":[221],"this":[222],"related":[224],"projects":[225],"NMR":[228],"EM":[230],"realms":[231],"continues":[234],"publicly":[240],"available":[241],"structural":[242],"data.":[243]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
