{"id":"https://openalex.org/W2970925136","doi":"https://doi.org/10.1186/s12859-019-3003-2","title":"Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization","display_name":"Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization","publication_year":2019,"publication_date":"2019-08-28","ids":{"openalex":"https://openalex.org/W2970925136","doi":"https://doi.org/10.1186/s12859-019-3003-2","mag":"2970925136","pmid":"https://pubmed.ncbi.nlm.nih.gov/31455212"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3003-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3003-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3003-2","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/track/pdf/10.1186/s12859-019-3003-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083435019","display_name":"Yongchun L\u00fc","orcid":null},"institutions":[{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yongchun L\u00fc","raw_affiliation_strings":["Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China. lvyongchun@ncic.ac.cn","Key Laboratory of Intelligent Information Processing, CAS, Beijing, China. lvyongchun@ncic.ac.cn","University of Chinese Academy of Sciences, Beijing, China. lvyongchun@ncic.ac.cn","University of Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China. lvyongchun@ncic.ac.cn","institution_ids":["https://openalex.org/I4210090176"]},{"raw_affiliation_string":"Key Laboratory of Intelligent Information Processing, CAS, Beijing, China. lvyongchun@ncic.ac.cn","institution_ids":["https://openalex.org/I4210108629"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China. lvyongchun@ncic.ac.cn","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086172600","display_name":"Xiangrui Zeng","orcid":"https://orcid.org/0000-0002-8589-4474"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiangrui Zeng","raw_affiliation_strings":["Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109472257","display_name":"Xiaofang Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaofang Zhao","raw_affiliation_strings":["Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China","University of Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046925429","display_name":"Shirui Li","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shirui Li","raw_affiliation_strings":["Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China","Key Laboratory of Intelligent Information Processing, CAS, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"raw_affiliation_string":"Key Laboratory of Intelligent Information Processing, CAS, Beijing, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100714089","display_name":"Hua Li","orcid":"https://orcid.org/0000-0003-4982-6455"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hua Li","raw_affiliation_strings":["Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China","Key Laboratory of Intelligent Information Processing, CAS, Beijing, China","University of Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"raw_affiliation_string":"Key Laboratory of Intelligent Information Processing, CAS, Beijing, China","institution_ids":[]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100618900","display_name":"Xin Gao","orcid":"https://orcid.org/0000-0002-7108-3574"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Xin Gao","raw_affiliation_strings":["King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000807861","display_name":"Min Xu","orcid":"https://orcid.org/0000-0002-0881-5891"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Min Xu","raw_affiliation_strings":["Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA. mxu1@cs.cmu.edu","Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA. mxu1@cs.cmu.edu","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5083435019"],"corresponding_institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I4210108629","https://openalex.org/I4210165038"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.8715,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.82223509,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"20","issue":"1","first_page":"443","last_page":"443"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9918000102043152,"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"}},"topics":[{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9918000102043152,"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/T11183","display_name":"Advanced X-ray Imaging Techniques","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/3108","display_name":"Radiation"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12039","display_name":"Electron and X-Ray Spectroscopy Techniques","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/2508","display_name":"Surfaces, Coatings and Films"},"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/computer-science","display_name":"Computer science","score":0.6928540468215942},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5321288108825684},{"id":"https://openalex.org/keywords/message-passing-interface","display_name":"Message Passing Interface","score":0.46261364221572876},{"id":"https://openalex.org/keywords/cryo-electron-tomography","display_name":"Cryo-electron tomography","score":0.4509706497192383},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.4340163767337799},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34930163621902466},{"id":"https://openalex.org/keywords/tomography","display_name":"Tomography","score":0.2257469892501831},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.18530893325805664},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1582202911376953},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.1377110481262207},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.1314239501953125}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6928540468215942},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5321288108825684},{"id":"https://openalex.org/C166782233","wikidata":"https://www.wikidata.org/wiki/Q127879","display_name":"Message Passing Interface","level":3,"score":0.46261364221572876},{"id":"https://openalex.org/C2777993257","wikidata":"https://www.wikidata.org/wiki/Q904576","display_name":"Cryo-electron tomography","level":3,"score":0.4509706497192383},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.4340163767337799},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34930163621902466},{"id":"https://openalex.org/C163716698","wikidata":"https://www.wikidata.org/wiki/Q841267","display_name":"Tomography","level":2,"score":0.2257469892501831},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.18530893325805664},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1582202911376953},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.1377110481262207},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.1314239501953125},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C854659","wikidata":"https://www.wikidata.org/wiki/Q1859284","display_name":"Message passing","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D018834","descriptor_name":"Chaperonin 60","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D018834","descriptor_name":"Chaperonin 60","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D018834","descriptor_name":"Chaperonin 60","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D018835","descriptor_name":"Chaperonin 10","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D018835","descriptor_name":"Chaperonin 10","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D018835","descriptor_name":"Chaperonin 10","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D055032","descriptor_name":"Electron Microscope Tomography","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055032","descriptor_name":"Electron Microscope Tomography","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055032","descriptor_name":"Electron Microscope Tomography","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059629","descriptor_name":"Signal-To-Noise Ratio","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059629","descriptor_name":"Signal-To-Noise Ratio","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059629","descriptor_name":"Signal-To-Noise Ratio","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-019-3003-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3003-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3003-2","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:31455212","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31455212","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:doaj.org/article:5e8f9fe0706f45488d62216dfa8c7b20","is_oa":true,"landing_page_url":"https://doaj.org/article/5e8f9fe0706f45488d62216dfa8c7b20","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 20, Iss 1, Pp 1-13 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6712796","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6712796","pdf_url":null,"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:repository.kaust.edu.sa:10754/656676","is_oa":true,"landing_page_url":"http://hdl.handle.net/10754/656676","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"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":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3003-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3003-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3003-2","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/G1120352242","display_name":null,"funder_award_id":"URF/1/3007-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G3385248028","display_name":null,"funder_award_id":"2017YFB1002703","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5188192957","display_name":null,"funder_award_id":"P41 GM103712","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5207768667","display_name":null,"funder_award_id":"P41 GM103712","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5353306443","display_name":null,"funder_award_id":"URF/1/2602-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G6380147298","display_name":null,"funder_award_id":"GM103712","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320310207","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33"},{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"},{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337968","display_name":"Center for Machine Learning and Health, School of Computer Science, Carnegie Mellon University","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2970925136.pdf","grobid_xml":"https://content.openalex.org/works/W2970925136.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W47135330","https://openalex.org/W1535035979","https://openalex.org/W1967925377","https://openalex.org/W1981765976","https://openalex.org/W1985983127","https://openalex.org/W1989585427","https://openalex.org/W1993858653","https://openalex.org/W1996074267","https://openalex.org/W2007653169","https://openalex.org/W2016367858","https://openalex.org/W2017292564","https://openalex.org/W2021009195","https://openalex.org/W2042455841","https://openalex.org/W2049137651","https://openalex.org/W2049330043","https://openalex.org/W2054520331","https://openalex.org/W2075824676","https://openalex.org/W2077345869","https://openalex.org/W2081460107","https://openalex.org/W2086449672","https://openalex.org/W2105875671","https://openalex.org/W2118620951","https://openalex.org/W2122151115","https://openalex.org/W2123207418","https://openalex.org/W2155071107","https://openalex.org/W2155539714","https://openalex.org/W2158957977","https://openalex.org/W2265299935","https://openalex.org/W2604272474","https://openalex.org/W2618381588","https://openalex.org/W2736743735","https://openalex.org/W2765581320","https://openalex.org/W2796200979","https://openalex.org/W2800645345","https://openalex.org/W2804850298","https://openalex.org/W2883376187","https://openalex.org/W2931162162","https://openalex.org/W2959668520","https://openalex.org/W2964322448","https://openalex.org/W4246936399","https://openalex.org/W4292907187","https://openalex.org/W4301734701"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2027972911","https://openalex.org/W2146343568","https://openalex.org/W2013643406","https://openalex.org/W2157978810","https://openalex.org/W2597809628","https://openalex.org/W4200215346"],"abstract_inverted_index":{"Cryo-electron":[0],"tomography":[1,34],"(Cryo-ET)":[2],"is":[3,167],"an":[4],"imaging":[5],"technique":[6],"used":[7],"to":[8,21,56,73,140,246],"generate":[9],"three-dimensional":[10,30,103],"structures":[11,228],"of":[12,29,32,66,100,122,179,229],"cellular":[13],"macromolecule":[14],"complexes":[15],"in":[16,102,125,138],"their":[17],"native":[18],"environment.":[19],"Due":[20],"developing":[22],"cryo-electron":[23,33],"microscopy":[24],"technology,":[25],"the":[26,69,96,120,171,182,224,249],"image":[27],"quality":[28],"reconstruction":[31],"has":[35],"greatly":[36],"improved.":[37],"However,":[38],"cryo-ET":[39],"images":[40],"are":[41,85],"characterized":[42],"by":[43],"low":[44,50,213],"resolution,":[45,62],"partial":[46],"data":[47,178,227],"loss":[48],"and":[49,60,76,82,98,159,208,231,243],"signal-to-noise":[51],"ratio":[52],"(SNR).":[53],"In":[54,105],"order":[55,139],"tackle":[57],"these":[58],"challenges":[59],"improve":[61],"a":[63,110,130,212],"large":[64],"number":[65],"subtomograms":[67,84,101,226],"containing":[68],"same":[70],"structure":[71],"needs":[72],"be":[74],"aligned":[75],"averaged.":[77],"Existing":[78],"methods":[79],"for":[80,118],"refining":[81],"aligning":[83],"still":[86],"highly":[87],"time-consuming,":[88],"requiring":[89],"many":[90],"computationally":[91],"intensive":[92],"processing":[93],"steps":[94],"(i.e.":[95],"rotations":[97],"translations":[99],"space).":[104],"this":[106],"article,":[107],"we":[108],"propose":[109],"Stochastic":[111],"Average":[112],"Gradient":[113],"(SAG)":[114],"fine-grained":[115,150,164,193,237],"alignment":[116,151,158,165,194,207,210,238],"method":[117,195],"optimizing":[119],"sum":[121],"dissimilarity":[123],"measure":[124],"real":[126],"space.":[127],"We":[128,144],"introduce":[129],"Message":[131],"Passing":[132],"Interface":[133],"(MPI)":[134],"parallel":[135,191,235],"programming":[136],"model":[137],"explore":[141],"further":[142],"speedup.":[143],"compare":[145],"our":[146,190,234],"stochastic":[147],"average":[148],"gradient":[149],"algorithm":[152,166],"with":[153,201,216],"two":[154,172,250],"baseline":[155,173,251],"methods,":[156],"high-precision":[157,206],"fast":[160,209],"alignment.":[161],"Our":[162],"SAG":[163],"much":[168],"faster":[169],"than":[170,204,248],"methods.":[174,252],"Results":[175],"on":[176],"simulated":[177],"GroEL":[180,230],"from":[181],"Protein":[183],"Data":[184],"Bank":[185],"(PDB":[186],"ID:1KP8)":[187],"showed":[188],"that":[189],"SAG-based":[192,236],"could":[196],"achieve":[197,240],"close-to-optimal":[198],"rigid":[199],"transformations":[200],"higher":[202,241],"precision":[203,242],"both":[205],"at":[211],"SNR":[214],"(SNR=0.003)":[215],"tilt":[217],"angle":[218],"range":[219],"\u00b160\u2218":[220],"or":[221],"\u00b140\u2218.":[222],"For":[223],"experimental":[225],"GroEL/GroES":[232],"complexes,":[233],"can":[239],"fewer":[244],"iterations":[245],"converge":[247]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
