{"id":"https://openalex.org/W4387080911","doi":"https://doi.org/10.1093/bioinformatics/btad587","title":"Simulating structurally variable nuclear pore complexes for microscopy","display_name":"Simulating structurally variable nuclear pore complexes for microscopy","publication_year":2023,"publication_date":"2023-09-26","ids":{"openalex":"https://openalex.org/W4387080911","doi":"https://doi.org/10.1093/bioinformatics/btad587","pmid":"https://pubmed.ncbi.nlm.nih.gov/37756700"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad587","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad587","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad587/51770594/btad587.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad587/51770594/btad587.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047679022","display_name":"M. Thei\u00df","orcid":"https://orcid.org/0000-0002-7843-2351"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Maria Theiss","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton, CB10 1SD, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-7843-2351","affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton, CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013600096","display_name":"Jean-Karim H\u00e8rich\u00e9","orcid":"https://orcid.org/0000-0001-6867-9425"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jean-Karim H\u00e9rich\u00e9","raw_affiliation_strings":["Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"],"raw_orcid":"https://orcid.org/0000-0001-6867-9425","affiliations":[{"raw_affiliation_string":"Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","institution_ids":["https://openalex.org/I4210153543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084747017","display_name":"Craig Russell","orcid":"https://orcid.org/0000-0002-2447-5911"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Craig Russell","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton, CB10 1SD, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton, CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026925673","display_name":"David Helekal","orcid":"https://orcid.org/0000-0002-9319-7097"},"institutions":[{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David Helekal","raw_affiliation_strings":["Centre for Doctoral Training in Mathematics for Real-World Systems, University of Warwick , Coventry CV4 7AL, United Kingdom","Centre for Doctoral Training in Mathematics for Real-World Systems, University of Warwick, Coventry, CV4 7AL, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Doctoral Training in Mathematics for Real-World Systems, University of Warwick , Coventry CV4 7AL, United Kingdom","institution_ids":["https://openalex.org/I39555362"]},{"raw_affiliation_string":"Centre for Doctoral Training in Mathematics for Real-World Systems, University of Warwick, Coventry, CV4 7AL, United Kingdom","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071171059","display_name":"Alisdair Soppitt","orcid":null},"institutions":[{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alisdair Soppitt","raw_affiliation_strings":["EPSRC Centre for Doctoral Training in Modelling of Heterogeneous Systems, University of Warwick , Coventry CV4 7AL, United Kingdom","EPSRC Centre for Doctoral Training in Modelling of Heterogeneous Systems, University of Warwick, Coventry, CV4 7AL, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EPSRC Centre for Doctoral Training in Modelling of Heterogeneous Systems, University of Warwick , Coventry CV4 7AL, United Kingdom","institution_ids":["https://openalex.org/I39555362"]},{"raw_affiliation_string":"EPSRC Centre for Doctoral Training in Modelling of Heterogeneous Systems, University of Warwick, Coventry, CV4 7AL, United Kingdom","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I39555362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028735345","display_name":"Jonas Ries","orcid":"https://orcid.org/0000-0002-6640-9250"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I2802916955","display_name":"Max Perutz Labs","ror":"https://ror.org/05cz70a34","country_code":"AT","type":"facility","lineage":["https://openalex.org/I2802916955"]},{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["AT","DE"],"is_corresponding":false,"raw_author_name":"Jonas Ries","raw_affiliation_strings":["Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","Max Perutz Labs, University of Vienna, Department of Structural and Computational Biology, Dr.-Bohr-Gasse 9, Vienna 1030, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","institution_ids":["https://openalex.org/I4210153543"]},{"raw_affiliation_string":"Max Perutz Labs, University of Vienna, Department of Structural and Computational Biology, Dr.-Bohr-Gasse 9, Vienna 1030, Austria","institution_ids":["https://openalex.org/I129774422","https://openalex.org/I2802916955"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043267985","display_name":"Jan Ellenberg","orcid":"https://orcid.org/0000-0001-5909-701X"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jan Ellenberg","raw_affiliation_strings":["Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","institution_ids":["https://openalex.org/I4210153543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081419327","display_name":"Alvis Br\u0101zma","orcid":"https://orcid.org/0000-0001-5988-7409"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alvis Brazma","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton, CB10 1SD, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton, CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034638851","display_name":"Virginie Uhlmann","orcid":"https://orcid.org/0000-0002-2859-9241"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Virginie Uhlmann","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton, CB10 1SD, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-2859-9241","affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton, CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5047679022"],"corresponding_institution_ids":["https://openalex.org/I1303153112"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2812,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.51161783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"39","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11841","display_name":"Nuclear Structure and Function","score":0.9836999773979187,"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/T11841","display_name":"Nuclear Structure and Function","score":0.9836999773979187,"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/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.004699999932199717,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.0027000000700354576,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6152592301368713},{"id":"https://openalex.org/keywords/replicate","display_name":"Replicate","score":0.5575681924819946},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.5357605218887329},{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.5264706611633301},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.5243406891822815},{"id":"https://openalex.org/keywords/nuclear-pore","display_name":"Nuclear pore","score":0.48453372716903687},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.46677297353744507},{"id":"https://openalex.org/keywords/ground-truth","display_name":"Ground truth","score":0.42645081877708435},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41191965341567993},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39253854751586914},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.340820848941803},{"id":"https://openalex.org/keywords/cytoplasm","display_name":"Cytoplasm","score":0.31341874599456787},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.26959216594696045},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18704521656036377},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.17413318157196045},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.15935418009757996},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14360541105270386}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6152592301368713},{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.5575681924819946},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5357605218887329},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.5264706611633301},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.5243406891822815},{"id":"https://openalex.org/C126725582","wikidata":"https://www.wikidata.org/wiki/Q30679","display_name":"Nuclear pore","level":3,"score":0.48453372716903687},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.46677297353744507},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.42645081877708435},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41191965341567993},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39253854751586914},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.340820848941803},{"id":"https://openalex.org/C190062978","wikidata":"https://www.wikidata.org/wiki/Q79899","display_name":"Cytoplasm","level":2,"score":0.31341874599456787},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.26959216594696045},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18704521656036377},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.17413318157196045},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.15935418009757996},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14360541105270386},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000072760","descriptor_name":"Single Molecule Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000072760","descriptor_name":"Single Molecule Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000072760","descriptor_name":"Single Molecule Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000072760","descriptor_name":"Single Molecule Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","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":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":"D022022","descriptor_name":"Nuclear Pore","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D022022","descriptor_name":"Nuclear Pore","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D022022","descriptor_name":"Nuclear Pore","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D022022","descriptor_name":"Nuclear Pore","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D022022","descriptor_name":"Nuclear Pore","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D022022","descriptor_name":"Nuclear Pore","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D022022","descriptor_name":"Nuclear Pore","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D022022","descriptor_name":"Nuclear Pore","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D028861","descriptor_name":"Nuclear Pore Complex Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D028861","descriptor_name":"Nuclear Pore Complex Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D028861","descriptor_name":"Nuclear Pore Complex Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D028861","descriptor_name":"Nuclear Pore Complex Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D028861","descriptor_name":"Nuclear Pore Complex Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D028861","descriptor_name":"Nuclear Pore Complex Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D028861","descriptor_name":"Nuclear Pore Complex Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D028861","descriptor_name":"Nuclear Pore Complex Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad587","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad587","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad587/51770594/btad587.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37756700","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37756700","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},{"id":"pmh:oai:pubmedcentral.nih.gov:10570993","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10570993","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10570993/pdf/btad587.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad587","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad587","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad587/51770594/btad587.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5562500205","display_name":null,"funder_award_id":"212962/Z/18/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4387080911.pdf"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1985868337","https://openalex.org/W1999399453","https://openalex.org/W2001976437","https://openalex.org/W2025739869","https://openalex.org/W2066521860","https://openalex.org/W2109591624","https://openalex.org/W2110534399","https://openalex.org/W2122614523","https://openalex.org/W2220896177","https://openalex.org/W2291672038","https://openalex.org/W2335825911","https://openalex.org/W2606299484","https://openalex.org/W2725753104","https://openalex.org/W2790485917","https://openalex.org/W2806399642","https://openalex.org/W2888051165","https://openalex.org/W2899354026","https://openalex.org/W2934437784","https://openalex.org/W2936155958","https://openalex.org/W2976942992","https://openalex.org/W3049234579","https://openalex.org/W3075072369","https://openalex.org/W3081651558","https://openalex.org/W3081964167","https://openalex.org/W3110617960","https://openalex.org/W3129122964","https://openalex.org/W3159354973","https://openalex.org/W3161404264","https://openalex.org/W3171694514","https://openalex.org/W3176144469","https://openalex.org/W3177828909","https://openalex.org/W3207915361","https://openalex.org/W3211957066","https://openalex.org/W3212208195","https://openalex.org/W3216930177","https://openalex.org/W4281687351","https://openalex.org/W4282936228","https://openalex.org/W4286203340","https://openalex.org/W4311677805"],"related_works":["https://openalex.org/W4254851101","https://openalex.org/W3171007296","https://openalex.org/W22115721","https://openalex.org/W2211931904","https://openalex.org/W2321234655","https://openalex.org/W2065444835","https://openalex.org/W4394550905","https://openalex.org/W2470062578","https://openalex.org/W2952773340","https://openalex.org/W2981861370"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,29],"nuclear":[2],"pore":[3],"complex":[4],"(NPC)":[5],"is":[6,24,77,85,216],"the":[7,71,97,127,153,221,234],"only":[8],"passageway":[9],"for":[10],"macromolecules":[11],"between":[12],"nucleus":[13],"and":[14,16,26,142,200],"cytoplasm,":[15],"an":[17],"important":[18],"reference":[19,174],"standard":[20],"in":[21],"microscopy:":[22],"it":[23,84],"massive":[25],"stereotypically":[27],"arranged.":[28],"average":[30],"architecture":[31],"of":[32,49,74,96,118,126,147,163,176,196,205,223,236],"NPC":[33,43,68,140,154,198],"proteins":[34],"has":[35],"been":[36],"resolved":[37],"with":[38,185],"pseudoatomic":[39],"precision,":[40],"however":[41],"observed":[42,212],"heterogeneities":[44],"evidence":[45],"a":[46,111,144,156,182,193,203],"high":[47,91],"degree":[48],"divergence":[50],"from":[51,94],"this":[52,75],"average.":[53],"Single-molecule":[54],"localization":[55],"microscopy":[56],"(SMLM)":[57],"images":[58],"NPCs":[59,121],"at":[60],"protein-level":[61],"resolution,":[62],"whereupon":[63],"image":[64,81,224],"analysis":[65,82,195,225],"software":[66],"studies":[67],"variability.":[69],"However,":[70],"true":[72,128],"picture":[73],"variability":[76,95,207],"unknown.":[78],"In":[79],"quantitative":[80],"experiments,":[83],"thus":[86],"difficult":[87],"to":[88,211,219,230],"distinguish":[89],"intrinsically":[90],"SMLM":[92],"noise":[93],"underlying":[98],"structure.":[99],"RESULTS:":[100],"We":[101,150],"introduce":[102],"CIR4MICS":[103],"('ceramics',":[104],"Configurable,":[105],"Irregular":[106],"Rings":[107],"FOR":[108],"MICroscopy":[109],"Simulations),":[110],"pipeline":[112],"that":[113,159,202],"synthesizes":[114],"ground":[115],"truth":[116],"datasets":[117,175],"structurally":[119],"variable":[120],"based":[122],"on":[123],"architectural":[124],"models":[125],"NPC.":[129],"Users":[130],"can":[131,209],"select":[132],"one":[133],"or":[134,137],"more":[135],"N-":[136],"C-terminally":[138],"tagged":[139],"proteins,":[141],"simulate":[143,166],"wide":[145],"range":[146,204],"geometric":[148,194],"variations.":[149,169],"also":[151],"represent":[152],"as":[155,227,229],"spring-model":[157],"such":[158],"arbitrary":[160],"deforming":[161],"forces,":[162],"user-defined":[164],"magnitudes,":[165],"irregularly":[167],"shaped":[168],"Further,":[170],"we":[171,190],"provide":[172],"annotated":[173],"simulated":[177,206],"human":[178],"NPCs,":[179],"which":[180],"facilitate":[181],"side-by-side":[183],"comparison":[184],"real":[186,197],"data.":[187],"To":[188],"demonstrate,":[189],"synthetically":[191],"replicate":[192],"radii":[199],"reveal":[201],"parameters":[208],"lead":[210],"results.":[213],"Our":[214],"simulator":[215],"therefore":[217],"valuable":[218],"test":[220],"capabilities":[222],"methods,":[226],"well":[228],"inform":[231],"experimentalists":[232],"about":[233],"requirements":[235],"hypothesis-driven":[237],"imaging":[238],"studies.":[239],"AVAILABILITY":[240],"AND":[241],"IMPLEMENTATION:":[242],"Code:":[243],"https://github.com/uhlmanngroup/cir4mics.":[244],"Simulated":[245],"data:":[246],"BioStudies":[247],"S-BSST1058.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
