{"id":"https://openalex.org/W3127416413","doi":"https://doi.org/10.1038/s42256-020-00290-y","title":"Extraction of protein dynamics information from cryo-EM maps using deep learning","display_name":"Extraction of protein dynamics information from cryo-EM maps using deep learning","publication_year":2021,"publication_date":"2021-02-04","ids":{"openalex":"https://openalex.org/W3127416413","doi":"https://doi.org/10.1038/s42256-020-00290-y","mag":"3127416413"},"language":"en","primary_location":{"id":"doi:10.1038/s42256-020-00290-y","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-020-00290-y","pdf_url":"https://www.nature.com/articles/s42256-020-00290-y.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://www.nature.com/articles/s42256-020-00290-y.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053913367","display_name":"Shigeyuki Matsumoto","orcid":"https://orcid.org/0000-0001-9329-6362"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shigeyuki Matsumoto","raw_affiliation_strings":["Medical Sciences Innovation Hub Program, RIKEN Cluster for Science, Technology and Innovation Hub, Tsurumi-ku, Kanagawa, Japan"],"affiliations":[{"raw_affiliation_string":"Medical Sciences Innovation Hub Program, RIKEN Cluster for Science, Technology and Innovation Hub, Tsurumi-ku, Kanagawa, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023231952","display_name":"Shoichi Ishida","orcid":"https://orcid.org/0000-0002-5638-3579"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shoichi Ishida","raw_affiliation_strings":["Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023816779","display_name":"Mitsugu Araki","orcid":"https://orcid.org/0000-0002-7810-4905"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Mitsugu Araki","raw_affiliation_strings":["Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068293662","display_name":"Takayuki Kato","orcid":"https://orcid.org/0000-0002-8879-6685"},"institutions":[{"id":"https://openalex.org/I4210152009","display_name":"Protein Research Foundation","ror":"https://ror.org/03yzv7g36","country_code":"JP","type":"other","lineage":["https://openalex.org/I4210152009"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takayuki Kato","raw_affiliation_strings":["Institute for Protein Research, Osaka University, Osaka, Japan"],"affiliations":[{"raw_affiliation_string":"Institute for Protein Research, Osaka University, Osaka, Japan","institution_ids":["https://openalex.org/I4210152009","https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072608872","display_name":"Kei Terayama","orcid":"https://orcid.org/0000-0003-3914-248X"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4210126580","display_name":"RIKEN Center for Advanced Intelligence Project","ror":"https://ror.org/03ckxwf91","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210126580"]},{"id":"https://openalex.org/I89630735","display_name":"Yokohama City University","ror":"https://ror.org/0135d1r83","country_code":"JP","type":"education","lineage":["https://openalex.org/I89630735"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kei Terayama","raw_affiliation_strings":["Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Kanagawa, Japan","Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan","Medical Sciences Innovation Hub Program, RIKEN Cluster for Science, Technology and Innovation Hub, Tsurumi-ku, Kanagawa, Japan","RIKEN Center for Advanced Intelligence Project, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Kanagawa, Japan","institution_ids":["https://openalex.org/I89630735"]},{"raw_affiliation_string":"Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"Medical Sciences Innovation Hub Program, RIKEN Cluster for Science, Technology and Innovation Hub, Tsurumi-ku, Kanagawa, Japan","institution_ids":[]},{"raw_affiliation_string":"RIKEN Center for Advanced Intelligence Project, Tokyo, Japan","institution_ids":["https://openalex.org/I4210126580"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046211758","display_name":"Yasushi Okuno","orcid":"https://orcid.org/0000-0003-3596-4208"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasushi Okuno","raw_affiliation_strings":["Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan","Medical Sciences Innovation Hub Program, RIKEN Cluster for Science, Technology and Innovation Hub, Tsurumi-ku, Kanagawa, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"Medical Sciences Innovation Hub Program, RIKEN Cluster for Science, Technology and Innovation Hub, Tsurumi-ku, Kanagawa, Japan","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5072608872"],"corresponding_institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4210126580","https://openalex.org/I89630735"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":12.0228,"has_fulltext":true,"cited_by_count":82,"citation_normalized_percentile":{"value":0.98897638,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"3","issue":"2","first_page":"153","last_page":"160"},"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":1.0,"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":1.0,"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/T12039","display_name":"Electron and X-Ray Spectroscopy Techniques","score":0.9970999956130981,"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"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9778000116348267,"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/cryo-electron-microscopy","display_name":"Cryo-electron microscopy","score":0.832094132900238},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6228874921798706},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5859174728393555},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5245532989501953},{"id":"https://openalex.org/keywords/protein-dynamics","display_name":"Protein dynamics","score":0.5012197494506836},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45797866582870483},{"id":"https://openalex.org/keywords/resolution","display_name":"Resolution (logic)","score":0.44103366136550903},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.43679025769233704},{"id":"https://openalex.org/keywords/biomolecular-structure","display_name":"Biomolecular structure","score":0.42050987482070923},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4001469612121582},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.38156044483184814},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.37744566798210144},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3655754327774048},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.31135058403015137},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.21785855293273926},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17597341537475586},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1179206371307373},{"id":"https://openalex.org/keywords/nuclear-magnetic-resonance","display_name":"Nuclear magnetic resonance","score":0.07068771123886108}],"concepts":[{"id":"https://openalex.org/C20702342","wikidata":"https://www.wikidata.org/wiki/Q5190506","display_name":"Cryo-electron microscopy","level":2,"score":0.832094132900238},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6228874921798706},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5859174728393555},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5245532989501953},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.5012197494506836},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45797866582870483},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.44103366136550903},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.43679025769233704},{"id":"https://openalex.org/C38111792","wikidata":"https://www.wikidata.org/wiki/Q15712714","display_name":"Biomolecular structure","level":3,"score":0.42050987482070923},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4001469612121582},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.38156044483184814},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.37744566798210144},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3655754327774048},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.31135058403015137},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.21785855293273926},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17597341537475586},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1179206371307373},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.07068771123886108},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1038/s42256-020-00290-y","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-020-00290-y","pdf_url":"https://www.nature.com/articles/s42256-020-00290-y.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1038/s42256-020-00290-y","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-020-00290-y","pdf_url":"https://www.nature.com/articles/s42256-020-00290-y.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1069223013","display_name":null,"funder_award_id":"JSPS KAKENHI","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G2481130354","display_name":null,"funder_award_id":"JP17K15106","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G3459562248","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4062414879","display_name":null,"funder_award_id":"JSPS KAKENHI","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G4227499671","display_name":null,"funder_award_id":"KAKENHI Grant","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4636223006","display_name":null,"funder_award_id":"JSPS KAK","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5786340949","display_name":null,"funder_award_id":"KAKENHI Grant Number","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7599130655","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G778570544","display_name":"Elucidation of functional mechanism based on the dynamic properties for the ongene products Ras","funder_award_id":"17K15106","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8430481527","display_name":null,"funder_award_id":"Number","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3127416413.pdf","grobid_xml":"https://content.openalex.org/works/W3127416413.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1920022804","https://openalex.org/W1983364832","https://openalex.org/W2001923477","https://openalex.org/W2028841370","https://openalex.org/W2035460215","https://openalex.org/W2039175603","https://openalex.org/W2057477511","https://openalex.org/W2059013803","https://openalex.org/W2066962978","https://openalex.org/W2067174909","https://openalex.org/W2081693079","https://openalex.org/W2086812659","https://openalex.org/W2100455255","https://openalex.org/W2127697948","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2161605421","https://openalex.org/W2211722331","https://openalex.org/W2296686360","https://openalex.org/W2301358467","https://openalex.org/W2336892636","https://openalex.org/W2340685884","https://openalex.org/W2343172899","https://openalex.org/W2397429809","https://openalex.org/W2463220226","https://openalex.org/W2608353599","https://openalex.org/W2623055862","https://openalex.org/W2736403501","https://openalex.org/W2753860285","https://openalex.org/W2762161295","https://openalex.org/W2765231623","https://openalex.org/W2784274035","https://openalex.org/W2786623728","https://openalex.org/W2809748575","https://openalex.org/W2883831643","https://openalex.org/W2885630788","https://openalex.org/W2889085087","https://openalex.org/W2892113269","https://openalex.org/W2894056527","https://openalex.org/W2894693380","https://openalex.org/W2904682577","https://openalex.org/W2924375708","https://openalex.org/W2939032800","https://openalex.org/W2942817778","https://openalex.org/W2945617528","https://openalex.org/W2950630354","https://openalex.org/W2955168413","https://openalex.org/W2962701388","https://openalex.org/W2963977738","https://openalex.org/W2965115627","https://openalex.org/W2966489898","https://openalex.org/W2970462530","https://openalex.org/W2971559235","https://openalex.org/W2972127712","https://openalex.org/W2974815351","https://openalex.org/W2980541278","https://openalex.org/W2990999848","https://openalex.org/W3007643904","https://openalex.org/W3009335299","https://openalex.org/W3016761449","https://openalex.org/W3102692458","https://openalex.org/W3105982350","https://openalex.org/W4252440583"],"related_works":["https://openalex.org/W2772226369","https://openalex.org/W2165360887","https://openalex.org/W2027077329","https://openalex.org/W4396730717","https://openalex.org/W2378801510","https://openalex.org/W4313310778","https://openalex.org/W4321487086","https://openalex.org/W4207031286","https://openalex.org/W2010414728","https://openalex.org/W2290574198"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":22},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}