{"id":"https://openalex.org/W2144047278","doi":"https://doi.org/10.1093/bioinformatics/15.10.807","title":"An analysis of the Protein Data Bank in search of temporal and global trends.","display_name":"An analysis of the Protein Data Bank in search of temporal and global trends.","publication_year":1999,"publication_date":"1999-10-01","ids":{"openalex":"https://openalex.org/W2144047278","doi":"https://doi.org/10.1093/bioinformatics/15.10.807","mag":"2144047278","pmid":"https://pubmed.ncbi.nlm.nih.gov/10705434"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/15.10.807","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/15.10.807","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/15/10/807/48837596/bioinformatics_15_10_807.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/15/10/807/48837596/bioinformatics_15_10_807.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013371163","display_name":"Helge Weissig","orcid":null},"institutions":[{"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":false,"raw_author_name":"H Weissig","raw_affiliation_strings":["San Diego Supercomputer Center, La Jolla, CA, USA","[San Diego Supercomputer Center, La Jolla, CA, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"San Diego Supercomputer Center, La Jolla, CA, USA","institution_ids":["https://openalex.org/I181653535"]},{"raw_affiliation_string":"[San Diego Supercomputer Center, La Jolla, CA, USA]","institution_ids":["https://openalex.org/I181653535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075833022","display_name":"Philip E. Bourne","orcid":"https://orcid.org/0000-0002-7618-7292"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"P E Bourne","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.4749,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.89772491,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"15","issue":"10","first_page":"807","last_page":"831"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.30250000953674316,"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":0.30250000953674316,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.057999998331069946,"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":0.0551999993622303,"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/computer-science","display_name":"Computer science","score":0.5421475172042847},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3501535654067993},{"id":"https://openalex.org/keywords/econometrics","display_name":"Econometrics","score":0.3394387364387512},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13351210951805115}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5421475172042847},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3501535654067993},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.3394387364387512},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13351210951805115}],"mesh":[{"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"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":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000639","qualifier_name":"trends","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/15.10.807","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/15.10.807","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/15/10/807/48837596/bioinformatics_15_10_807.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:10705434","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/10705434","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/15.10.807","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/15.10.807","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/15/10/807/48837596/bioinformatics_15_10_807.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation","score":0.7200000286102295}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"MOTIVATION:":[0],"Biological":[1],"databases,":[2],"with":[3,230],"their":[4],"rapidly":[5],"expanding":[6],"contents,":[7],"are":[8,118,123],"indispensable":[9],"tools":[10],"in":[11,46,71,85,104,120,208,233],"the":[12,44,59,66,69,79,94,97,105,114,132,139,145,154,169,176,188,213,216,220,226,231],"quest":[13],"to":[14,64,77,81,222],"understand":[15],"more":[16,160,224],"about":[17],"biological":[18,210],"function.":[19,211],"However,":[20],"a":[21,25,29,36,55,150,157,234],"serious":[22],"user":[23,177],"of":[24,32,50,68,88,100,134,147,156,163,171,178,192,215,225],"database":[26],"that":[27,184,236],"comprises":[28],"large":[30],"collection":[31],"data,":[33,181],"collected":[34,136],"over":[35,93],"long":[37],"period,":[38],"will":[39],"likely":[40],"be":[41,198],"struck":[42],"by":[43,168],"inconsistency":[45],"reporting":[47,138],"individual":[48],"items":[49],"data.":[51,90,174],"This":[52],"paper":[53],"takes":[54],"critical":[56],"look":[57],"at":[58],"Protein":[60],"Data":[61],"Bank":[62],"(PDB)":[63],"explore":[65,78],"seriousness":[67],"problem":[70],"one":[72],"particular":[73],"data":[74,122,135,228],"set":[75],"and":[76,131,194],"implications":[80],"those":[82],"actively":[83],"engaged":[84],"comparative":[86],"analysis":[87,162],"these":[89,164],"RESULTS:":[91],"Averaged":[92],"complete":[95],"corpus,":[96],"stereochemical":[98],"quality":[99,155,190],"atomic":[101],"models":[102],"has,":[103],"past":[106],"few":[107],"years,":[108],"moved":[109],"towards":[110],"ideal":[111],"values.":[112],"At":[113],"same":[115],"time,":[116],"there":[117],"inconsistencies":[119,165],"how":[121],"reported.":[124],"Water":[125],"content":[126],"is":[127,166],"not":[128],"reported":[129],"consistently":[130],"percent":[133],"when":[137,200],"high-resolution":[140],"shell":[141],"varies,":[142],"detracting":[143],"from":[144],"value":[146,196],"resolution":[148,193],"as":[149],"yardstick":[151],"for":[152,204],"assessing":[153],"structure.":[158],"A":[159],"detailed":[161],"hampered":[167],"lack":[170],"machine-readable":[172],"experimental":[173,227],"To":[175,212],"macromolecular":[179],"structure":[180],"this":[182,218],"suggests":[183,219],"structural":[185],"details":[186],"beyond":[187],"standard":[189],"measures":[191],"R":[195],"should":[197],"considered":[199],"using":[201],"coordinate":[202],"sets":[203],"further":[205],"derivation":[206],"or":[207],"inferring":[209],"curators":[214],"PDB,":[217],"need":[221],"capture":[223],"associated":[229],"experiment":[232],"way":[235],"permits":[237],"straightforward":[238],"parsing.":[239]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
