{"id":"https://openalex.org/W3192986217","doi":"https://doi.org/10.1021/acs.jcim.1c00602","title":"Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns","display_name":"Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns","publication_year":2021,"publication_date":"2021-08-06","ids":{"openalex":"https://openalex.org/W3192986217","doi":"https://doi.org/10.1021/acs.jcim.1c00602","mag":"3192986217","pmid":"https://pubmed.ncbi.nlm.nih.gov/34357759"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00602","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00602","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.1c00602","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064384115","display_name":"Sandhya P. Tiwari","orcid":"https://orcid.org/0000-0002-0747-3826"},"institutions":[{"id":"https://openalex.org/I113306721","display_name":"Hiroshima University","ror":"https://ror.org/03t78wx29","country_code":"JP","type":"education","lineage":["https://openalex.org/I113306721"]},{"id":"https://openalex.org/I4210129730","display_name":"RIKEN Center for Computational Science","ror":"https://ror.org/03r519674","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210129730"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Sandhya P. Tiwari","raw_affiliation_strings":["Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8521, Japan","RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8521, Japan","institution_ids":["https://openalex.org/I113306721"]},{"raw_affiliation_string":"RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan","institution_ids":["https://openalex.org/I4210129730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090638713","display_name":"Florence Tama","orcid":"https://orcid.org/0000-0003-2021-5618"},"institutions":[{"id":"https://openalex.org/I4210129730","display_name":"RIKEN Center for Computational Science","ror":"https://ror.org/03r519674","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210129730"]},{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Florence Tama","raw_affiliation_strings":["Graduate School of Science, Department of Physics, Nagoya University, Nagoya, Aichi 464-8601, Japan","Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Aichi 464-8601, Japan","RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan"],"raw_orcid":"https://orcid.org/0000-0003-2021-5618","affiliations":[{"raw_affiliation_string":"Graduate School of Science, Department of Physics, Nagoya University, Nagoya, Aichi 464-8601, Japan","institution_ids":["https://openalex.org/I60134161"]},{"raw_affiliation_string":"Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Aichi 464-8601, Japan","institution_ids":["https://openalex.org/I60134161"]},{"raw_affiliation_string":"RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan","institution_ids":["https://openalex.org/I4210129730"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036207834","display_name":"Osamu Miyashita","orcid":"https://orcid.org/0000-0002-2530-5674"},"institutions":[{"id":"https://openalex.org/I4210129730","display_name":"RIKEN Center for Computational Science","ror":"https://ror.org/03r519674","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210129730"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Osamu Miyashita","raw_affiliation_strings":["RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan","institution_ids":["https://openalex.org/I4210129730"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5036207834","https://openalex.org/A5090638713"],"corresponding_institution_ids":["https://openalex.org/I4210129730","https://openalex.org/I60134161"],"apc_list":null,"apc_paid":null,"fwci":0.0801,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.34587257,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"61","issue":"8","first_page":"4108","last_page":"4119"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9988999962806702,"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/T11183","display_name":"Advanced X-ray Imaging Techniques","score":0.9983000159263611,"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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9966999888420105,"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/diffraction","display_name":"Diffraction","score":0.8504496812820435},{"id":"https://openalex.org/keywords/electron-diffraction","display_name":"Electron diffraction","score":0.4738643169403076},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.47371333837509155},{"id":"https://openalex.org/keywords/scattering","display_name":"Scattering","score":0.4602104723453522},{"id":"https://openalex.org/keywords/orientation","display_name":"Orientation (vector space)","score":0.45596522092819214},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.44536417722702026},{"id":"https://openalex.org/keywords/x-ray-crystallography","display_name":"X-ray crystallography","score":0.44194090366363525},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.40797844529151917},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3898550271987915},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.38388264179229736},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.3748599886894226},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3380935788154602},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24261143803596497},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23963332176208496},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2007436752319336},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.16308817267417908}],"concepts":[{"id":"https://openalex.org/C207114421","wikidata":"https://www.wikidata.org/wiki/Q133900","display_name":"Diffraction","level":2,"score":0.8504496812820435},{"id":"https://openalex.org/C77557913","wikidata":"https://www.wikidata.org/wiki/Q864822","display_name":"Electron diffraction","level":3,"score":0.4738643169403076},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.47371333837509155},{"id":"https://openalex.org/C191486275","wikidata":"https://www.wikidata.org/wiki/Q210028","display_name":"Scattering","level":2,"score":0.4602104723453522},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.45596522092819214},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.44536417722702026},{"id":"https://openalex.org/C50515024","wikidata":"https://www.wikidata.org/wiki/Q826582","display_name":"X-ray crystallography","level":3,"score":0.44194090366363525},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.40797844529151917},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3898550271987915},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.38388264179229736},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3748599886894226},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3380935788154602},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24261143803596497},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23963332176208496},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2007436752319336},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.16308817267417908},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003460","descriptor_name":"Crystallization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003460","descriptor_name":"Crystallization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003460","descriptor_name":"Crystallization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007834","descriptor_name":"Lasers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007834","descriptor_name":"Lasers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007834","descriptor_name":"Lasers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014961","descriptor_name":"X-Ray Diffraction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014961","descriptor_name":"X-Ray Diffraction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014961","descriptor_name":"X-Ray Diffraction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c00602","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00602","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:34357759","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34357759","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.1c00602","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00602","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6190775326","display_name":null,"funder_award_id":"Kakenhi 20H05453","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1911270099","https://openalex.org/W1988662633","https://openalex.org/W2035460215","https://openalex.org/W2051567790","https://openalex.org/W2055453593","https://openalex.org/W2056026917","https://openalex.org/W2070183703","https://openalex.org/W2084069427","https://openalex.org/W2091968034","https://openalex.org/W2136470366","https://openalex.org/W2261998615","https://openalex.org/W2297637824","https://openalex.org/W2563699184","https://openalex.org/W2608153289","https://openalex.org/W2612715625","https://openalex.org/W2613580110","https://openalex.org/W2625886940","https://openalex.org/W2763641211","https://openalex.org/W2774559011","https://openalex.org/W2788385968","https://openalex.org/W2793039150","https://openalex.org/W2799756241","https://openalex.org/W2806303695","https://openalex.org/W2890339033","https://openalex.org/W2890628869","https://openalex.org/W2891475202","https://openalex.org/W2892069134","https://openalex.org/W2894460353","https://openalex.org/W2898192617","https://openalex.org/W2917173873","https://openalex.org/W2967243986","https://openalex.org/W2968494487","https://openalex.org/W3005553970","https://openalex.org/W3011881575","https://openalex.org/W3014108899","https://openalex.org/W3032464302","https://openalex.org/W3035965352","https://openalex.org/W3047820180","https://openalex.org/W3093254596","https://openalex.org/W3099878876","https://openalex.org/W4244057438"],"related_works":["https://openalex.org/W1972035260","https://openalex.org/W4301594054","https://openalex.org/W2794488505","https://openalex.org/W3125889879","https://openalex.org/W3124422538","https://openalex.org/W2295467472","https://openalex.org/W3046451053","https://openalex.org/W2097909533","https://openalex.org/W2144398666","https://openalex.org/W1973479238"],"abstract_inverted_index":{"70S":[0],"ribosome":[1],"complex),":[2],"and":[3,71,114],"EMD-5152":[4],"(budding":[5],"yeast":[6],"Nup84":[7],"complex).":[8],"We":[9],"observed":[10],"that":[11,48],"choosing":[12],"the":[13,21,34,41,49,56,61,66,72,81,115,118,122,129],"best":[14],"strategy":[15],"to":[16],"define":[17],"matching":[18,29],"regions":[19],"on":[20,55],"diffraction":[22,30,38,69,130],"patterns":[23,39,70],"is":[24],"critical":[25],"for":[26,89,93,103],"identifying":[27],"correctly":[28],"patterns.":[31,131],"While":[32],"increasing":[33],"number":[35],"of":[36,60,74,97,109,117,121,124],"input":[37,68],"improved":[40],"matches":[42,51],"in":[43,65,80],"some":[44],"cases,":[45],"we":[46],"found":[47],"resulting":[50],"are":[52],"more":[53],"dependent":[54],"uniqueness":[57],"or":[58],"complexity":[59],"shape":[62,79],"as":[63,126],"captured":[64,127],"individual":[67],"availability":[73],"a":[75,94,106],"similar":[76],"3D":[77],"biological":[78],"search":[82],"library.":[83],"The":[84],"protocol":[85],"could":[86],"be":[87],"useful":[88],"finding":[90],"candidate":[91],"models":[92],"limited":[95],"amount":[96],"low-resolution":[98],"data,":[99],"even":[100],"when":[101],"insufficient":[102],"reconstruction,":[104],"performing":[105],"quick":[107],"exploration":[108],"new":[110],"data":[111],"upon":[112],"collection,":[113],"analysis":[116],"conformational":[119],"heterogeneity":[120],"particle":[123],"interest":[125],"within":[128]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-12T08:28:47.272897","created_date":"2025-10-10T00:00:00"}