{"id":"https://openalex.org/W4226017322","doi":"https://doi.org/10.1371/journal.pcbi.1009578","title":"Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations","display_name":"Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations","publication_year":2022,"publication_date":"2022-04-05","ids":{"openalex":"https://openalex.org/W4226017322","doi":"https://doi.org/10.1371/journal.pcbi.1009578","pmid":"https://pubmed.ncbi.nlm.nih.gov/35381009"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009578","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009578","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009578&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009578&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022307899","display_name":"Cheng Tan","orcid":"https://orcid.org/0000-0002-8957-4267"},"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":"Cheng Tan","raw_affiliation_strings":["Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan"],"raw_orcid":"https://orcid.org/0000-0002-8957-4267","affiliations":[{"raw_affiliation_string":"Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan","institution_ids":["https://openalex.org/I4210129730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048153247","display_name":"Jaewoon Jung","orcid":"https://orcid.org/0000-0002-2285-4432"},"institutions":[{"id":"https://openalex.org/I4210110652","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652"]},{"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":"Jaewoon Jung","raw_affiliation_strings":["Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan","Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan"],"raw_orcid":"https://orcid.org/0000-0002-2285-4432","affiliations":[{"raw_affiliation_string":"Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan","institution_ids":["https://openalex.org/I4210129730"]},{"raw_affiliation_string":"Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan","institution_ids":["https://openalex.org/I4210110652"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032436398","display_name":"Chigusa Kobayashi","orcid":"https://orcid.org/0000-0002-5603-4619"},"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":"Chigusa Kobayashi","raw_affiliation_strings":["Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan"],"raw_orcid":"https://orcid.org/0000-0002-5603-4619","affiliations":[{"raw_affiliation_string":"Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan","institution_ids":["https://openalex.org/I4210129730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061835859","display_name":"Diego Ugarte La Torre","orcid":"https://orcid.org/0000-0002-8391-8065"},"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":"Diego Ugarte La Torre","raw_affiliation_strings":["Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan"],"raw_orcid":"https://orcid.org/0000-0002-8391-8065","affiliations":[{"raw_affiliation_string":"Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan","institution_ids":["https://openalex.org/I4210129730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071626951","display_name":"Shoji Takada","orcid":"https://orcid.org/0000-0001-5385-7217"},"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":true,"raw_author_name":"Shoji Takada","raw_affiliation_strings":["Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0001-5385-7217","affiliations":[{"raw_affiliation_string":"Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074728289","display_name":"Yuji Sugita","orcid":"https://orcid.org/0000-0001-9738-9216"},"institutions":[{"id":"https://openalex.org/I4210110652","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652"]},{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]},{"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":"Yuji Sugita","raw_affiliation_strings":["Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan","Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan","Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan"],"raw_orcid":"https://orcid.org/0000-0001-9738-9216","affiliations":[{"raw_affiliation_string":"Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan","institution_ids":["https://openalex.org/I4210129730"]},{"raw_affiliation_string":"Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan","institution_ids":["https://openalex.org/I4210116810"]},{"raw_affiliation_string":"Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan","institution_ids":["https://openalex.org/I4210110652"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5022307899","https://openalex.org/A5032436398","https://openalex.org/A5048153247","https://openalex.org/A5061835859","https://openalex.org/A5071626951","https://openalex.org/A5074728289"],"corresponding_institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4210110652","https://openalex.org/I4210116810","https://openalex.org/I4210129730"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":6.1514,"has_fulltext":true,"cited_by_count":85,"citation_normalized_percentile":{"value":0.97643126,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"18","issue":"4","first_page":"e1009578","last_page":"e1009578"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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/T10604","display_name":"RNA Research and Splicing","score":0.9991999864578247,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9977999925613403,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6642228364944458},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5403066277503967},{"id":"https://openalex.org/keywords/brownian-dynamics","display_name":"Brownian dynamics","score":0.509425699710846},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.49749425053596497},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.497207909822464},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.45546257495880127},{"id":"https://openalex.org/keywords/molecular-biophysics","display_name":"Molecular biophysics","score":0.430670827627182},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.42436960339546204},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.34781724214553833},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32577353715896606},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.31235751509666443},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.30357450246810913},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.296217679977417},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.24428606033325195},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12782049179077148},{"id":"https://openalex.org/keywords/brownian-motion","display_name":"Brownian motion","score":0.12369820475578308}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6642228364944458},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5403066277503967},{"id":"https://openalex.org/C130603088","wikidata":"https://www.wikidata.org/wiki/Q4976526","display_name":"Brownian dynamics","level":3,"score":0.509425699710846},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.49749425053596497},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.497207909822464},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.45546257495880127},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.430670827627182},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.42436960339546204},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.34781724214553833},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32577353715896606},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.31235751509666443},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.30357450246810913},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.296217679977417},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.24428606033325195},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12782049179077148},{"id":"https://openalex.org/C112401455","wikidata":"https://www.wikidata.org/wiki/Q178036","display_name":"Brownian motion","level":2,"score":0.12369820475578308},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1009578","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009578","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009578&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:35381009","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35381009","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:a853c17c404e4022af5f41aa197f3225","is_oa":false,"landing_page_url":"https://doaj.org/article/a853c17c404e4022af5f41aa197f3225","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 4, p e1009578 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9012402","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9012402","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009578","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009578","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009578&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1153619429","display_name":null,"funder_award_id":"hp200129","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G1527142388","display_name":null,"funder_award_id":"JPMXP1020200101","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G1683304399","display_name":null,"funder_award_id":"21H05282","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G2003449856","display_name":null,"funder_award_id":"hp200028","funder_id":"https://openalex.org/F4320335125","funder_display_name":"RIKEN"},{"id":"https://openalex.org/G2719384493","display_name":null,"funder_award_id":"19H05645","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G2991958618","display_name":null,"funder_award_id":"21H05249","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4150949267","display_name":null,"funder_award_id":"hp210172","funder_id":"https://openalex.org/F4320335125","funder_display_name":"RIKEN"},{"id":"https://openalex.org/G4332620356","display_name":null,"funder_award_id":"hp210177","funder_id":"https://openalex.org/F4320335125","funder_display_name":"RIKEN"},{"id":"https://openalex.org/G5046756818","display_name":null,"funder_award_id":"hp210177","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G5176219108","display_name":null,"funder_award_id":"19H05645","funder_id":"https://openalex.org/F4320335125","funder_display_name":"RIKEN"},{"id":"https://openalex.org/G5241674051","display_name":null,"funder_award_id":"21H05282","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7122904584","display_name":null,"funder_award_id":"21H05249","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G7493608361","display_name":null,"funder_award_id":"hp210172","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G7574485952","display_name":null,"funder_award_id":"hp200135","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G760910490","display_name":"Multi-scale molecular dynamics simulation on biomolecular dynamics in crowded cellular environments","funder_award_id":"19H05645","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8389989449","display_name":null,"funder_award_id":"hp200135","funder_id":"https://openalex.org/F4320335125","funder_display_name":"RIKEN"},{"id":"https://openalex.org/G8949051751","display_name":null,"funder_award_id":"JPMXP1020200201","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"}],"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"},{"id":"https://openalex.org/F4320335125","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4226017322.pdf","grobid_xml":"https://content.openalex.org/works/W4226017322.grobid-xml"},"referenced_works_count":108,"referenced_works":["https://openalex.org/W184563540","https://openalex.org/W1178456644","https://openalex.org/W1508256447","https://openalex.org/W1952608303","https://openalex.org/W1966431081","https://openalex.org/W1969937114","https://openalex.org/W1974035453","https://openalex.org/W1976660940","https://openalex.org/W1989274555","https://openalex.org/W1989925383","https://openalex.org/W1992898397","https://openalex.org/W2003949305","https://openalex.org/W2010713749","https://openalex.org/W2017635466","https://openalex.org/W2018783142","https://openalex.org/W2019465613","https://openalex.org/W2022022844","https://openalex.org/W2029667189","https://openalex.org/W2031742969","https://openalex.org/W2033355083","https://openalex.org/W2040809566","https://openalex.org/W2045533286","https://openalex.org/W2049424035","https://openalex.org/W2052022130","https://openalex.org/W2059906541","https://openalex.org/W2065864578","https://openalex.org/W2067204014","https://openalex.org/W2074140794","https://openalex.org/W2074718022","https://openalex.org/W2085978470","https://openalex.org/W2085989411","https://openalex.org/W2103107485","https://openalex.org/W2103653834","https://openalex.org/W2107303111","https://openalex.org/W2115005877","https://openalex.org/W2115659144","https://openalex.org/W2116682661","https://openalex.org/W2117275660","https://openalex.org/W2119267663","https://openalex.org/W2120575449","https://openalex.org/W2127522551","https://openalex.org/W2150329841","https://openalex.org/W2150981663","https://openalex.org/W2151553287","https://openalex.org/W2155276776","https://openalex.org/W2160544821","https://openalex.org/W2163647830","https://openalex.org/W2171546617","https://openalex.org/W2171695688","https://openalex.org/W2178631187","https://openalex.org/W2192231700","https://openalex.org/W2234216373","https://openalex.org/W2295059836","https://openalex.org/W2312589039","https://openalex.org/W2325241225","https://openalex.org/W2327560429","https://openalex.org/W2328004490","https://openalex.org/W2328563019","https://openalex.org/W2413334978","https://openalex.org/W2439976498","https://openalex.org/W2519618428","https://openalex.org/W2523898334","https://openalex.org/W2555870966","https://openalex.org/W2590568317","https://openalex.org/W2737764894","https://openalex.org/W2765424242","https://openalex.org/W2784384705","https://openalex.org/W2788194767","https://openalex.org/W2790216512","https://openalex.org/W2794696654","https://openalex.org/W2795843171","https://openalex.org/W2800801983","https://openalex.org/W2806024219","https://openalex.org/W2810076504","https://openalex.org/W2883604250","https://openalex.org/W2897203649","https://openalex.org/W2902587740","https://openalex.org/W2938491141","https://openalex.org/W2949308290","https://openalex.org/W2952390072","https://openalex.org/W2979035266","https://openalex.org/W2983190776","https://openalex.org/W2988716798","https://openalex.org/W2989052455","https://openalex.org/W2991405842","https://openalex.org/W2997226623","https://openalex.org/W2998133382","https://openalex.org/W3005177895","https://openalex.org/W3005188436","https://openalex.org/W3009501790","https://openalex.org/W3010929769","https://openalex.org/W3012524120","https://openalex.org/W3026054170","https://openalex.org/W3038184119","https://openalex.org/W3044361076","https://openalex.org/W3048619043","https://openalex.org/W3092787915","https://openalex.org/W3099479137","https://openalex.org/W3108187028","https://openalex.org/W3109509293","https://openalex.org/W3126756260","https://openalex.org/W3128698945","https://openalex.org/W3156859670","https://openalex.org/W3157810520","https://openalex.org/W3158393751","https://openalex.org/W3164215582","https://openalex.org/W3193187385","https://openalex.org/W3202422087"],"related_works":["https://openalex.org/W2946599741","https://openalex.org/W2593264178","https://openalex.org/W3171039768","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2058542300","https://openalex.org/W2043066834","https://openalex.org/W1564749278","https://openalex.org/W2294851134","https://openalex.org/W3215498386"],"abstract_inverted_index":{"Residue-level":[0],"coarse-grained":[1],"(CG)":[2],"models":[3,222],"have":[4],"become":[5],"one":[6,186],"of":[7,39,157,187,232],"the":[8,16,53,91,145,168,182,188,197,204],"most":[9],"popular":[10],"tools":[11],"in":[12,15,29,80,98,117,126,147,167,181,190,228],"biomolecular":[13,234],"simulations":[14,33,129,235,250],"trade-off":[17],"between":[18],"modeling":[19],"accuracy":[20],"and":[21,41,65,72,120,220,245],"computational":[22],"efficiency.":[23],"To":[24,143],"investigate":[25],"large-scale":[26,233],"biological":[27],"phenomena":[28],"molecular":[30],"dynamics":[31],"(MD)":[32],"with":[34,104,199,236],"CG":[35,61,87,110,127,148,191,238],"models,":[36,62],"unified":[37],"treatments":[38],"proteins":[40,119],"nucleic":[42,121],"acids,":[43],"as":[44,46,84,132,230,257],"well":[45],"efficient":[47],"parallel":[48],"computations,":[49],"are":[50,130,185],"indispensable.":[51],"In":[52],"GENESIS":[54,229],"MD":[55,128,149,192],"software,":[56],"we":[57,151,195],"implement":[58],"several":[59],"residue-level":[60,237],"covering":[63],"structure-based":[64],"context-based":[66],"potentials":[67],"for":[68,178],"both":[69,118],"well-folded":[70],"biomolecules":[71],"intrinsically":[73],"disordered":[74],"regions.":[75],"An":[76],"amino":[77],"acid":[78],"residue":[79],"protein":[81],"is":[82,102,159],"represented":[83],"a":[85,96,108,138,162],"single":[86,109],"particle":[88,111],"centered":[89],"at":[90],"C\u03b1":[92],"atom":[93],"position,":[94],"while":[95],"nucleotide":[97],"RNA":[99],"or":[100,209,261],"DNA":[101],"modeled":[103],"three":[105],"beads.":[106],"Then,":[107],"represents":[112],"around":[113],"ten":[114],"heavy":[115],"atoms":[116],"acids.":[122],"The":[123],"input":[124,134],"data":[125],"treated":[131],"GROMACS-style":[133],"files":[135],"generated":[136],"from":[137],"newly":[139],"developed":[140],"toolbox,":[141],"GENESIS-CG-tool.":[142],"optimize":[144],"performance":[146,205],"simulations,":[150],"utilize":[152],"multiple":[153],"neighbor":[154],"lists,":[155],"each":[156],"which":[158],"attached":[160],"to":[161,202,251],"different":[163],"nonbonded":[164],"interaction":[165],"potential":[166],"cell-linked":[169],"list":[170],"method.":[171],"We":[172,211],"found":[173],"that":[174],"random":[175],"number":[176],"generations":[177],"Gaussian":[179],"distributions":[180],"Langevin":[183],"thermostat":[184],"bottlenecks":[189],"simulations.":[193],"Therefore,":[194],"parallelize":[196],"computations":[198],"message-passing-interface":[200],"(MPI)":[201],"improve":[203],"on":[206],"PC":[207],"clusters":[208],"supercomputers.":[210],"simulate":[212],"Herpes":[213],"simplex":[214],"virus":[215],"(HSV)":[216],"type":[217],"2":[218],"B-capsid":[219],"chromatin":[221,259],"containing":[223],"more":[224],"than":[225],"1,000":[226],"nucleosomes":[227],"examples":[231],"models.":[239],"This":[240],"framework":[241],"extends":[242],"accessible":[243],"spatial":[244],"temporal":[246],"scales":[247],"by":[248],"multi-scale":[249],"study":[252],"biologically":[253],"relevant":[254],"phenomena,":[255],"such":[256],"genome-scale":[258],"folding":[260],"phase-separated":[262],"membrane-less":[263],"condensations.":[264]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":24},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":8}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}