{"id":"https://openalex.org/W4381337048","doi":"https://doi.org/10.1186/s12859-023-05388-9","title":"BeEM: fast and faithful conversion of mmCIF format structure files to PDB format","display_name":"BeEM: fast and faithful conversion of mmCIF format structure files to PDB format","publication_year":2023,"publication_date":"2023-06-20","ids":{"openalex":"https://openalex.org/W4381337048","doi":"https://doi.org/10.1186/s12859-023-05388-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/37340457"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05388-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05388-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05388-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05388-9","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/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chengxin Zhang","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA. zcx@umich.edu","Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA. zcx@umich.edu","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5101510848"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.7424,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.67040626,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"24","issue":"1","first_page":"260","last_page":"260"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.3073999881744385,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.3073999881744385,"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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.14970000088214874,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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":0.11710000038146973,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.9266703724861145},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.6947014927864075},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6939851641654968},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5861617922782898},{"id":"https://openalex.org/keywords/structural-bioinformatics","display_name":"Structural bioinformatics","score":0.4906705617904663},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4826424717903137},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.47324949502944946},{"id":"https://openalex.org/keywords/data-format","display_name":"Data format","score":0.44745486974716187},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.44165632128715515},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.36388352513313293},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.35815244913101196},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3284379243850708},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.17165270447731018},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.17108270525932312},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12997817993164062}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.9266703724861145},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.6947014927864075},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6939851641654968},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5861617922782898},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.4906705617904663},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4826424717903137},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.47324949502944946},{"id":"https://openalex.org/C2985331491","wikidata":"https://www.wikidata.org/wiki/Q5227298","display_name":"Data format","level":2,"score":0.44745486974716187},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.44165632128715515},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.36388352513313293},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35815244913101196},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3284379243850708},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.17165270447731018},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.17108270525932312},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12997817993164062},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05388-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05388-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05388-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37340457","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37340457","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10280956","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10280956","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10280956/pdf/12859_2023_Article_5388.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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:71e6b09d090148de9f15d046b8b1468e","is_oa":true,"landing_page_url":"https://doaj.org/article/71e6b09d090148de9f15d046b8b1468e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-6 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05388-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05388-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05388-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"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/G4006316252","display_name":"Track 1: ACCESS Resource Allocations Marketplace and Platform Services (RAMPS)","funder_award_id":"2138259","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"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/G465309803","display_name":null,"funder_award_id":"and #2138296","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"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/G792242950","display_name":null,"funder_award_id":"#2138259, #2138286, #2138307, #2137603, and #2138296","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"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/F4320337377","display_name":"Office of Advanced Cyberinfrastructure","ror":"https://ror.org/04nh1dc89"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4381337048.pdf"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1533059251","https://openalex.org/W2102245393","https://openalex.org/W2106648157","https://openalex.org/W2111270835","https://openalex.org/W2114850508","https://openalex.org/W2126103104","https://openalex.org/W2126341972","https://openalex.org/W2141920771","https://openalex.org/W2144998676","https://openalex.org/W2152326664","https://openalex.org/W2609813487","https://openalex.org/W2611792444","https://openalex.org/W2807540482","https://openalex.org/W2938821856","https://openalex.org/W2949223833","https://openalex.org/W2973457155","https://openalex.org/W3004214328","https://openalex.org/W3014576393","https://openalex.org/W3164046276","https://openalex.org/W3166524949","https://openalex.org/W4229042017","https://openalex.org/W4255594044","https://openalex.org/W4282922306","https://openalex.org/W4293475204"],"related_works":["https://openalex.org/W102940356","https://openalex.org/W2225560680","https://openalex.org/W2973523639","https://openalex.org/W3104537585","https://openalex.org/W4389309199","https://openalex.org/W2112585543","https://openalex.org/W2022374214","https://openalex.org/W2518314460","https://openalex.org/W2401430279","https://openalex.org/W4381337048"],"abstract_inverted_index":{"BACKGROUND:":[0],"Although":[1],"mmCIF":[2,43,60,79,110],"is":[3,27,49,119,141,154,165,175],"the":[4,17,23,29,135,138,142,178],"current":[5],"official":[6],"format":[7,26,32,80,162],"for":[8,33,137,160],"deposition":[9],"of":[10,117,134,144],"protein":[11,18],"and":[12,92,131,149,157],"nucleic":[13],"acid":[14],"structures":[15],"to":[16,41,46,56,83,111],"data":[19],"bank":[20],"(PDB)":[21],"database,":[22],"legacy":[24],"PDB":[25,47,84,112],"still":[28],"primary":[30],"supported":[31,106],"many":[34,59,65],"structural":[35,170],"bioinformatics":[36],"tools.":[37],"Therefore,":[38],"reliable":[39],"software":[40],"convert":[42,58],"structure":[44,81],"files":[45,48,82],"needed.":[50],"Unfortunately,":[51],"existing":[52,109,126],"conversion":[53,87,115,145],"programs":[54],"fail":[55],"correctly":[57],"files,":[61],"especially":[62],"those":[63],"with":[64,98],"atoms":[66],"and/or":[67],"long":[68],"chain":[69,93,96],"identifies.":[70],"RESULTS:":[71],"This":[72],"study":[73],"proposed":[74],"BeEM,":[75],"which":[76,103,164],"converts":[77],"any":[78,108],"format.":[85],"BeEM":[86,118,153],"faithfully":[88],"retains":[89],"all":[90],"atomic":[91],"information,":[94],"including":[95],"IDs":[97],"more":[99],"than":[100,125],"2":[101],"characters,":[102],"are":[104],"not":[105],"by":[107],"converters.":[113],"The":[114,172],"speed":[116,139],"at":[120,181],"least":[121],"ten":[122],"times":[123],"faster":[124],"converters":[127],"such":[128],"as":[129],"MAXIT":[130],"Phenix.":[132],"Part":[133],"reason":[136],"improvement":[140],"avoidance":[143],"between":[146],"numerical":[147],"values":[148],"text":[150],"strings.":[151],"CONCLUSION:":[152],"a":[155,166],"fast":[156],"accurate":[158],"tool":[159],"mmCIF-to-PDB":[161],"conversion,":[163],"common":[167],"procedure":[168],"in":[169],"biology.":[171],"source":[173],"code":[174],"available":[176],"under":[177],"BSD":[179],"licence":[180],"https://github.com/kad-ecoli/BeEM/":[182],".":[183]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
