{"id":"https://openalex.org/W4362515170","doi":"https://doi.org/10.1093/database/baad018","title":"PDC: a highly compact file format to store protein 3D coordinates","display_name":"PDC: a highly compact file format to store protein 3D coordinates","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W4362515170","doi":"https://doi.org/10.1093/database/baad018","pmid":"https://pubmed.ncbi.nlm.nih.gov/37010520"},"language":"en","primary_location":{"id":"doi:10.1093/database/baad018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baad018","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baad018/49731475/baad018.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","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/database/article-pdf/doi/10.1093/database/baad018/49731475/baad018.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101510848","display_name":"Chengxin Zhang","orcid":"https://orcid.org/0000-0001-7290-1324"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I199037182","display_name":"Washtenaw Community College","ror":"https://ror.org/03k77wm53","country_code":"US","type":"education","lineage":["https://openalex.org/I199037182"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I2801525552","display_name":"Whitney Museum of American Art","ror":"https://ror.org/01g1t6g78","country_code":"US","type":"archive","lineage":["https://openalex.org/I2801525552"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chengxin Zhang","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , 100 Washtenaw Av, Ann Arbor, MI 48109, USA","Department of Molecular, Cellular, and Developmental Biology, Yale University , 266 Whitney Av, New Haven, CT 06511, USA","Howard Hughes Medical Institute , 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA"],"raw_orcid":"https://orcid.org/0000-0001-7290-1324","affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , 100 Washtenaw Av, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I199037182","https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Molecular, Cellular, and Developmental Biology, Yale University , 266 Whitney Av, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I2801525552","https://openalex.org/I32971472"]},{"raw_affiliation_string":"Howard Hughes Medical Institute , 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA","institution_ids":["https://openalex.org/I1344073410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007909912","display_name":"Anna Marie Pyle","orcid":"https://orcid.org/0000-0001-9045-8872"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I2801525552","display_name":"Whitney Museum of American Art","ror":"https://ror.org/01g1t6g78","country_code":"US","type":"archive","lineage":["https://openalex.org/I2801525552"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anna Marie Pyle","raw_affiliation_strings":["Department of Chemistry, Yale University , 225 Prospect St, New Haven, CT 06511, USA","Department of Molecular, Cellular, and Developmental Biology, Yale University , 266 Whitney Av, New Haven, CT 06511, USA","Howard Hughes Medical Institute , 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Yale University , 225 Prospect St, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Molecular, Cellular, and Developmental Biology, Yale University , 266 Whitney Av, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I2801525552","https://openalex.org/I32971472"]},{"raw_affiliation_string":"Howard Hughes Medical Institute , 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA","institution_ids":["https://openalex.org/I1344073410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5101510848"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I199037182","https://openalex.org/I27837315","https://openalex.org/I2801525552","https://openalex.org/I32971472"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.2616,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.61856529,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"2023","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9962000250816345,"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":0.9908999800682068,"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":0.6987345218658447},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.5952860116958618},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4750266671180725},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4222230911254883},{"id":"https://openalex.org/keywords/compact-disc","display_name":"Compact disc","score":0.41419893503189087},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.40674668550491333},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3614085912704468}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6987345218658447},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.5952860116958618},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4750266671180725},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4222230911254883},{"id":"https://openalex.org/C504131036","wikidata":"https://www.wikidata.org/wiki/Q34467","display_name":"Compact disc","level":2,"score":0.41419893503189087},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.40674668550491333},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3614085912704468},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D030562","descriptor_name":"Databases, Protein","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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baad018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baad018","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baad018/49731475/baad018.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:37010520","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37010520","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10069377","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10069377","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10069377/pdf/baad018.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baad018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baad018","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baad018/49731475/baad018.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.800000011920929}],"awards":[{"id":"https://openalex.org/G1453181110","display_name":null,"funder_award_id":"#2138286","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G1912064254","display_name":"Track 4:  Advanced CI Coordination Ecosystem: Monitoring and Measurement Services","funder_award_id":"2137603","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3562386289","display_name":null,"funder_award_id":"#2138296","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G4010157413","display_name":null,"funder_award_id":"2138259","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G4676224565","display_name":"ACO: An Open CI Ecosystem to Advance Scientific Discovery (OpenCI)","funder_award_id":"2138296","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G509285653","display_name":"Track 3: COre National Ecosystem for CyberinfrasTructure (CONECT)","funder_award_id":"2138307","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5367127336","display_name":null,"funder_award_id":"#2138307","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G5464919783","display_name":null,"funder_award_id":"2137603","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G8300691027","display_name":"Track 2: Customized Multi-tier Assistance, Training, and Computational Help (MATCH) for End User ACCESS to CI","funder_award_id":"2138286","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/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320337377","display_name":"Office of Advanced Cyberinfrastructure","ror":"https://ror.org/04nh1dc89"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1987305898","https://openalex.org/W2011658408","https://openalex.org/W2049902088","https://openalex.org/W2126341972","https://openalex.org/W2604075160","https://openalex.org/W2611792444","https://openalex.org/W2950192635","https://openalex.org/W3093323969","https://openalex.org/W3177828909","https://openalex.org/W3183921815","https://openalex.org/W3186179742","https://openalex.org/W3211795435","https://openalex.org/W4206903088","https://openalex.org/W4224277640","https://openalex.org/W4293475204","https://openalex.org/W4388866605"],"related_works":["https://openalex.org/W4321141969","https://openalex.org/W4388355720","https://openalex.org/W2485106781","https://openalex.org/W4388355377","https://openalex.org/W2177826381","https://openalex.org/W2461801250","https://openalex.org/W2105814884","https://openalex.org/W2050916086","https://openalex.org/W2505596809","https://openalex.org/W1624557985"],"abstract_inverted_index":{"Recent":[0],"improvements":[1],"in":[2,13,56],"computational":[3],"and":[4,41,46,68,115,126,137],"experimental":[5],"techniques":[6],"for":[7,135],"obtaining":[8],"protein":[9,48],"structures":[10],"have":[11],"resulted":[12],"an":[14],"explosion":[15],"of":[16,26,44,52,100,105,130,139,142],"3D":[17],"coordinate":[18],"data.":[19,145],"To":[20],"cope":[21],"with":[22,75,97],"the":[23,32],"ever-increasing":[24],"sizes":[25,62,107],"structure":[27],"databases,":[28],"this":[29],"work":[30],"proposes":[31],"Protein":[33,64],"Data":[34,65],"Compression":[35],"(PDC)":[36],"format,":[37],"which":[38,102],"compresses":[39],"coordinates":[40],"temperature":[42],"factors":[43],"full-atomic":[45],"C\u03b1-only":[47],"structures.":[49,91],"Without":[50],"loss":[51],"precision,":[53,101],"PDC":[54,92,131],"results":[55],"69%":[57],"to":[58,89],"78%":[59],"smaller":[60],"file":[61,106],"than":[63,84],"Bank":[66],"(PDB)":[67],"macromolecular":[69,90],"Crystallographic":[70],"Information":[71],"File":[72],"(mmCIF)":[73],"files":[74],"standard":[76],"GZIP":[77],"compression.":[78],"It":[79],"uses":[80],"\u223c60%":[81],"less":[82],"space":[83],"existing":[85],"compression":[86,96],"algorithms":[87],"specific":[88],"optionally":[93],"performs":[94],"lossy":[95],"minimal":[98],"sacrifice":[99],"allows":[103],"reduction":[104],"by":[108],"another":[109],"79%.":[110],"Conversion":[111],"between":[112],"PDC,":[113],"mmCIF":[114],"PDB":[116],"formats":[117],"is":[118],"typically":[119],"achieved":[120],"within":[121],"0.02":[122],"s.":[123],"The":[124],"compactness":[125],"fast":[127],"reading/writing":[128],"speed":[129],"make":[132],"it":[133],"valuable":[134],"storage":[136],"analysis":[138],"large":[140],"quantity":[141],"tertiary":[143],"structural":[144],"Database":[146],"URL":[147],"https://github.com/kad-ecoli/pdc.":[148]},"counts_by_year":[{"year":2024,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
