{"id":"https://openalex.org/W2179263669","doi":"https://doi.org/10.1093/bioinformatics/btv543","title":"PyPDB: a Python API for the Protein Data Bank","display_name":"PyPDB: a Python API for the Protein Data Bank","publication_year":2015,"publication_date":"2015-09-14","ids":{"openalex":"https://openalex.org/W2179263669","doi":"https://doi.org/10.1093/bioinformatics/btv543","mag":"2179263669","pmid":"https://pubmed.ncbi.nlm.nih.gov/26369703"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv543","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv543","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/1/159/49016436/bioinformatics_32_1_159.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/32/1/159/49016436/bioinformatics_32_1_159.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090794745","display_name":"William Gilpin","orcid":"https://orcid.org/0000-0001-8666-6951"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"William Gilpin","raw_affiliation_strings":["Department of Applied Physics, Stanford University, Stanford, CA 94305, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Physics, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5090794745"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1371,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.47697915,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"32","issue":"1","first_page":"159","last_page":"160"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.3752000033855438,"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":0.3752000033855438,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.3370000123977661,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.058800000697374344,"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/python","display_name":"Python (programming language)","score":0.9134221076965332},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8233460187911987},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.7543336153030396},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.7008309960365295},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.6652421951293945},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.570507287979126},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.4557189643383026},{"id":"https://openalex.org/keywords/application-programming-interface","display_name":"Application programming interface","score":0.4359495937824249},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3731086254119873},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.34975460171699524},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3465091288089752},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.07158845663070679},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.06765082478523254}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9134221076965332},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8233460187911987},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7543336153030396},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.7008309960365295},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6652421951293945},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.570507287979126},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.4557189643383026},{"id":"https://openalex.org/C99613125","wikidata":"https://www.wikidata.org/wiki/Q165194","display_name":"Application programming interface","level":2,"score":0.4359495937824249},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3731086254119873},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.34975460171699524},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3465091288089752},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.07158845663070679},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.06765082478523254},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btv543","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv543","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/1/159/49016436/bioinformatics_32_1_159.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:26369703","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26369703","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/btv543","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv543","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/1/159/49016436/bioinformatics_32_1_159.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":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2179263669.pdf","grobid_xml":"https://content.openalex.org/works/W2179263669.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2102633320","https://openalex.org/W2114850508","https://openalex.org/W2122735960","https://openalex.org/W2130479394","https://openalex.org/W2139300598","https://openalex.org/W2163385116","https://openalex.org/W2168172687"],"related_works":["https://openalex.org/W2088162897","https://openalex.org/W2020669016","https://openalex.org/W2090630809","https://openalex.org/W2106612397","https://openalex.org/W2518314460","https://openalex.org/W2401430279","https://openalex.org/W2589205199","https://openalex.org/W2952811294","https://openalex.org/W2134815007","https://openalex.org/W4386448451"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"have":[2],"created":[3],"a":[4,22],"Python":[5,51,90],"programming":[6],"interface":[7],"for":[8,21,95],"the":[9,38,61,71,79,121],"RCSB":[10],"Protein":[11],"Data":[12],"Bank":[13],"(PDB)":[14],"that":[15,73],"allows":[16],"search":[17,69],"and":[18,30,42,55,120],"data":[19],"retrieval":[20],"wide":[23],"range":[24],"of":[25,67,70],"result":[26],"types,":[27,52],"including":[28,102],"BLAST":[29],"sequence":[31],"motif":[32],"queries.":[33],"The":[34,58,98,128],"API":[35,41,123],"relies":[36],"on":[37,135],"existing":[39],"XML-based":[40],"operates":[43],"by":[44],"creating":[45],"custom":[46],"XML":[47],"requests":[48],"from":[49],"native":[50],"allowing":[53],"extensibility":[54],"straightforward":[56],"modification.":[57],"package":[59],"has":[60],"ability":[62],"to":[63],"perform":[64],"many":[65],"types":[66],"advanced":[68],"PDB":[72,80],"are":[74],"otherwise":[75],"only":[76],"available":[77,109,134],"through":[78],"website.":[81],"AVAILABILITY":[82],"AND":[83],"IMPLEMENTATION:":[84],"PyPDB":[85],"is":[86,108,125,132],"implemented":[87],"exclusively":[88],"in":[89],"3":[91],"using":[92],"standard":[93],"libraries":[94],"maximal":[96],"compatibility.":[97],"most":[99],"up-to-date":[100],"version,":[101],"iPython":[103],"notebooks":[104],"containing":[105],"usage":[106],"tutorials,":[107],"free-of-charge":[110],"under":[111],"an":[112],"open-source":[113],"MIT":[114],"license":[115],"via":[116],"GitHub":[117],"at":[118,126],"https://github.com/williamgilpin/pypdb,":[119],"full":[122],"reference":[124],"http://williamgilpin.github.io/pypdb_docs/html/.":[127],"latest":[129],"stable":[130],"release":[131],"also":[133],"PyPI.":[136],"CONTACT:":[137],"wgilpin@stanford.edu.":[138]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}