{"id":"https://openalex.org/W2166458835","doi":"https://doi.org/10.1093/nar/gki057","title":"The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema","display_name":"The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema","publication_year":2004,"publication_date":"2004-12-17","ids":{"openalex":"https://openalex.org/W2166458835","doi":"https://doi.org/10.1093/nar/gki057","mag":"2166458835","pmid":"https://pubmed.ncbi.nlm.nih.gov/15608185"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki057","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki057","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D233/7621857/gki057.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/D233/7621857/gki057.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111986892","display_name":"N. Deshpande","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"N. Deshpande","raw_affiliation_strings":["San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","San Diego Supercomputer Center and"],"affiliations":[{"raw_affiliation_string":"San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"raw_affiliation_string":"San Diego Supercomputer Center and","institution_ids":["https://openalex.org/I181653535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5111986892"],"corresponding_institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":14.5905,"has_fulltext":true,"cited_by_count":346,"citation_normalized_percentile":{"value":0.99529585,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"33","issue":"Database issue","first_page":"D233","last_page":"D237"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9975000023841858,"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":0.9975000023841858,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9969000220298767,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9930999875068665,"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 (RCSB PDB)","score":0.890159010887146},{"id":"https://openalex.org/keywords/collaboratory","display_name":"Collaboratory","score":0.8349175453186035},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.790424644947052},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5406901240348816},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.5126118063926697},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4757366180419922},{"id":"https://openalex.org/keywords/structural-bioinformatics","display_name":"Structural bioinformatics","score":0.43488171696662903},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.407110333442688},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38197460770606995},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.33066707849502563},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.12670737504959106}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.890159010887146},{"id":"https://openalex.org/C2776787376","wikidata":"https://www.wikidata.org/wiki/Q5145870","display_name":"Collaboratory","level":2,"score":0.8349175453186035},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.790424644947052},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5406901240348816},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.5126118063926697},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4757366180419922},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.43488171696662903},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.407110333442688},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38197460770606995},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.33066707849502563},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.12670737504959106},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gki057","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki057","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D233/7621857/gki057.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:15608185","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15608185","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:alma.01RUT_INST:11664894000004646","is_oa":false,"landing_page_url":"https://scholarship.libraries.rutgers.edu/esploro/outputs/journalArticle/The-RCSB-Protein-Data-Bank-a/991031665439404646","pdf_url":null,"source":{"id":"https://openalex.org/S4210197018","display_name":"View","issn_l":"2688-268X","issn":["2688-268X","2688-3988"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:europepmc.org:163513","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC540011","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:540011","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/540011","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gki057","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki057","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D233/7621857/gki057.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":[{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320312581","display_name":"Rutgers, The State University of New Jersey","ror":null},{"id":"https://openalex.org/F4320316545","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07"},{"id":"https://openalex.org/F4320332178","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320332603","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2166458835.pdf","grobid_xml":"https://content.openalex.org/works/W2166458835.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W85390549","https://openalex.org/W1515171040","https://openalex.org/W1533059251","https://openalex.org/W1910105166","https://openalex.org/W1966041739","https://openalex.org/W1975197163","https://openalex.org/W2003144438","https://openalex.org/W2009696139","https://openalex.org/W2055043387","https://openalex.org/W2083334314","https://openalex.org/W2096525273","https://openalex.org/W2099235960","https://openalex.org/W2103017472","https://openalex.org/W2130479394","https://openalex.org/W2147809382","https://openalex.org/W2150306348","https://openalex.org/W2150556577","https://openalex.org/W2151430326","https://openalex.org/W2155480785","https://openalex.org/W2159482845","https://openalex.org/W2164277910","https://openalex.org/W4213149192","https://openalex.org/W4236236547","https://openalex.org/W4242739003"],"related_works":["https://openalex.org/W102940356","https://openalex.org/W2518314460","https://openalex.org/W2022374214","https://openalex.org/W2225560680","https://openalex.org/W2898364362","https://openalex.org/W3087678678","https://openalex.org/W2973523639","https://openalex.org/W1529796813","https://openalex.org/W3104537585","https://openalex.org/W2916669734"],"abstract_inverted_index":{"The":[0,18,39,50,97],"Protein":[1],"Data":[2],"Bank":[3],"(PDB)":[4],"is":[5,42,79],"the":[6,31,54,57,80,101,107],"central":[7],"worldwide":[8],"repository":[9],"for":[10,21,30],"three-dimensional":[11],"(3D)":[12],"structure":[13,37,62],"data":[14,63,85],"of":[15,35,56,84,100],"biological":[16],"macromolecules.":[17],"Research":[19],"Collaboratory":[20],"Structural":[22],"Bioinformatics":[23],"(RCSB)":[24],"has":[25],"completely":[26],"redesigned":[27],"its":[28],"resource":[29],"distribution":[32],"and":[33,67,71,82,94],"query":[34,70],"3D":[36],"data.":[38],"re-engineered":[40,102],"site":[41,52,59,110],"currently":[43],"in":[44,64,113],"public":[45],"beta":[46],"test":[47],"at":[48,111],"http://pdbbeta.rcsb.org.":[49],"new":[51,76],"expands":[53],"functionality":[55],"existing":[58],"by":[60],"providing":[61],"greater":[65],"detail":[66],"uniformity,":[68],"improved":[69],"enhanced":[72],"analysis":[73],"tools.":[74],"A":[75],"key":[77],"feature":[78],"integration":[81],"searchability":[83],"from":[86],"over":[87],"20":[88],"other":[89],"sources":[90],"covering":[91],"genomic,":[92],"proteomic":[93],"disease":[95],"relationships.":[96],"current":[98],"capabilities":[99],"site,":[103],"which":[104],"will":[105],"become":[106],"RCSB":[108],"production":[109],"http://www.pdb.org":[112],"late":[114],"2005,":[115],"are":[116],"described.":[117]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":22},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":18},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":17}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
