{"id":"https://openalex.org/W4403096503","doi":"https://doi.org/10.1021/acs.jcim.4c01467","title":"BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation","display_name":"BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation","publication_year":2024,"publication_date":"2024-10-03","ids":{"openalex":"https://openalex.org/W4403096503","doi":"https://doi.org/10.1021/acs.jcim.4c01467","pmid":"https://pubmed.ncbi.nlm.nih.gov/39361452"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01467","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01467","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01467?ref=article_openPDF","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://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01467?ref=article_openPDF","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061267883","display_name":"Takunori Yasuda","orcid":"https://orcid.org/0009-0003-9423-0957"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Takunori Yasuda","raw_affiliation_strings":["Doctoral Program in Biology, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan"],"raw_orcid":"https://orcid.org/0009-0003-9423-0957","affiliations":[{"raw_affiliation_string":"Doctoral Program in Biology, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054539747","display_name":"Rikuri Morita","orcid":"https://orcid.org/0000-0002-0465-5528"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Rikuri Morita","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan"],"raw_orcid":"https://orcid.org/0000-0002-0465-5528","affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048994262","display_name":"Yasuteru Shigeta","orcid":"https://orcid.org/0000-0002-3219-6007"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasuteru Shigeta","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan"],"raw_orcid":"https://orcid.org/0000-0002-3219-6007","affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034873036","display_name":"Ryuhei Harada","orcid":"https://orcid.org/0000-0001-7987-0540"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Ryuhei Harada","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan"],"raw_orcid":"https://orcid.org/0000-0001-7987-0540","affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5034873036","https://openalex.org/A5061267883"],"corresponding_institution_ids":["https://openalex.org/I146399215"],"apc_list":null,"apc_paid":null,"fwci":0.16,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.49657319,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"64","issue":"19","first_page":"7184","last_page":"7188"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9975000023841858,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9951000213623047,"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":0.6771873831748962},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4969692528247833},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.43360787630081177},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37419068813323975},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2683483958244324},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16980361938476562},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.16907429695129395},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.14550286531448364}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6771873831748962},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4969692528247833},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.43360787630081177},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37419068813323975},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2683483958244324},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16980361938476562},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.16907429695129395},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.14550286531448364},{"id":"https://openalex.org/C19417346","wikidata":"https://www.wikidata.org/wiki/Q7922","display_name":"Pedagogy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"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},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c01467","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01467","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01467?ref=article_openPDF","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:39361452","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39361452","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},{"id":"pmh:oai:pubmedcentral.nih.gov:11481083","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11481083","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11481083/pdf/ci4c01467.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c01467","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01467","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01467?ref=article_openPDF","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/G2582532162","display_name":null,"funder_award_id":"JP23H04879","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4686155070","display_name":null,"funder_award_id":"JP22KJ0421","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5442299985","display_name":null,"funder_award_id":"JP23H02427","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6306952216","display_name":"\u751f\u4f53\u819c\u306e\u4e21\u89aa\u5a92\u52b9\u679c\u3092\u53d6\u308a\u8fbc\u3093\u3060\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u624b\u6cd5\u306e\u958b\u767a","funder_award_id":"23K16989","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G710677904","display_name":"\u5206\u5b50\u52d5\u529b\u5b66\u8a08\u7b97\u306b\u57fa\u3065\u304f\u30ce\u30f3\u30b3\u30fc\u30c7\u30a3\u30f3\u30b0RNA\u306e\u7acb\u4f53\u69cb\u9020\u4e88\u6e2c","funder_award_id":"22KJ0421","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7560602839","display_name":null,"funder_award_id":"JP21K06094","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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403096503.pdf","grobid_xml":"https://content.openalex.org/works/W4403096503.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1911566730","https://openalex.org/W1968958227","https://openalex.org/W2003949305","https://openalex.org/W2012500478","https://openalex.org/W2056672534","https://openalex.org/W2062279255","https://openalex.org/W2066736364","https://openalex.org/W2082199388","https://openalex.org/W2085872842","https://openalex.org/W2110670340","https://openalex.org/W2121400889","https://openalex.org/W2140194072","https://openalex.org/W2152442148","https://openalex.org/W2160171025","https://openalex.org/W2169678694","https://openalex.org/W2313038686","https://openalex.org/W2324294207","https://openalex.org/W2329727879","https://openalex.org/W2540491215","https://openalex.org/W2542660070","https://openalex.org/W2616655501","https://openalex.org/W2740546874","https://openalex.org/W2802429563","https://openalex.org/W2968787565","https://openalex.org/W2969567271","https://openalex.org/W2973734810","https://openalex.org/W2998103913","https://openalex.org/W3024385728","https://openalex.org/W3081651558","https://openalex.org/W3124703980","https://openalex.org/W3157668468","https://openalex.org/W3176856228","https://openalex.org/W3196570262","https://openalex.org/W3207915361","https://openalex.org/W4206528648","https://openalex.org/W4212888384","https://openalex.org/W4214530410","https://openalex.org/W4282984361","https://openalex.org/W4294001680","https://openalex.org/W4303969070","https://openalex.org/W4315783827","https://openalex.org/W4317104064","https://openalex.org/W4385064136","https://openalex.org/W4387440676","https://openalex.org/W4392504719","https://openalex.org/W4400082588","https://openalex.org/W4401644825"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W4402327032","https://openalex.org/W1773535258"],"abstract_inverted_index":{"Understanding":[0],"the":[1,4,37,63,88,113,120,132,151],"influence":[2],"of":[3,115],"cellular":[5,38],"environment":[6,39],"on":[7,70,150,182],"protein":[8,14,117,127],"conformations":[9,118],"is":[10,74],"crucial":[11],"for":[12,136,178],"elucidating":[13],"functions":[15],"within":[16,90],"living":[17],"cells.":[18],"In":[19],"studies":[20,52],"using":[21],"molecular":[22],"dynamics":[23],"(MD)":[24],"simulation,":[25],"carbon":[26],"nanotubes":[27],"and":[28,48,79,104,111,126,140,142,160,174],"hydrophobic":[29,57],"cages":[30],"have":[31],"been":[32],"widely":[33],"used":[34],"to":[35,76,87],"emulate":[36],"inside":[40,66],"specific":[41],"large":[42],"biomolecules":[43],"such":[44],"as":[45],"ribosome":[46],"tunnels":[47],"chaperones.":[49],"However,":[50],"recent":[51],"suggest":[53],"that":[54,101],"these":[55,71],"uniform":[56],"models":[58,81,106],"may":[59],"not":[60],"adequately":[61],"capture":[62],"environmental":[64],"effects":[65],"each":[67],"biomolecule.":[68],"Based":[69],"facts,":[72],"it":[73],"necessary":[75],"generate":[77],"spherical":[78,103],"cylindrical":[80,105],"with":[82,107,131],"varied":[83],"chemical":[84,109],"properties":[85,110],"corresponding":[86,133],"components":[89],"target":[91],"biomolecules.":[92],"We":[93],"developed":[94],"a":[95,163,175],"biomolecular":[96],"environment-mimicking":[97],"model":[98,125],"generator":[99],"(BEMM-GEN)":[100],"generates":[102],"user-specified":[108],"allows":[112],"integration":[114],"arbitrary":[116],"into":[119],"generated":[121,152],"models.":[122],"BEMM-GEN":[123,155],"provides":[124],"complex":[128],"structures,":[129],"along":[130],"parameter":[134],"files":[135,173],"MD":[137,147],"simulation":[138,148],"(AMBER":[139],"GROMACS),":[141],"users":[143],"immediately":[144],"run":[145],"their":[146],"based":[149],"input":[153],"files.":[154],"can":[156],"be":[157],"freely":[158],"downloaded":[159],"installed":[161],"via":[162],"Python":[164],"package":[165],"manager":[166],"(pip":[167],"install":[168],"BEMM-gen).":[169],"The":[170],"source":[171],"code":[172],"user":[176],"manual":[177],"operation":[179],"are":[180],"provided":[181],"GitHub":[183],"(https://github.com/y4suda/BEMM-GEN).":[184]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
