{"id":"https://openalex.org/W4410287206","doi":"https://doi.org/10.1021/acs.jcim.5c00069","title":"Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems","display_name":"Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems","publication_year":2025,"publication_date":"2025-05-12","ids":{"openalex":"https://openalex.org/W4410287206","doi":"https://doi.org/10.1021/acs.jcim.5c00069","pmid":"https://pubmed.ncbi.nlm.nih.gov/40354253"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00069","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00069","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","license_id":"https://openalex.org/licenses/cc-by","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.5c00069","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5105022303","display_name":"Mikkel D. Andreasen","orcid":null},"institutions":[{"id":"https://openalex.org/I204337017","display_name":"Aarhus University","ror":"https://ror.org/01aj84f44","country_code":"DK","type":"education","lineage":["https://openalex.org/I204337017"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Mikkel D. Andreasen","raw_affiliation_strings":["Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark","institution_ids":["https://openalex.org/I204337017"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017675228","display_name":"Paulo C. T. Souza","orcid":"https://orcid.org/0000-0003-0660-1301"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Paulo C. T. Souza","raw_affiliation_strings":["Centre Blaise Pascal de Simulation et de Mod\u00e9lisation Num\u00e9rique, Ecole Normale Sup\u00e9rieure de Lyon, 6 all\u00e9e d\u2019Italie, 69364 Lyon, France","Laboratoire de Biologie et Mod\u00e9lisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, Ecole Normale Sup\u00e9rieure de Lyon, 46 all\u00e9e d\u2019Italie, 69364 Lyon, France"],"affiliations":[{"raw_affiliation_string":"Centre Blaise Pascal de Simulation et de Mod\u00e9lisation Num\u00e9rique, Ecole Normale Sup\u00e9rieure de Lyon, 6 all\u00e9e d\u2019Italie, 69364 Lyon, France","institution_ids":["https://openalex.org/I113428412"]},{"raw_affiliation_string":"Laboratoire de Biologie et Mod\u00e9lisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, Ecole Normale Sup\u00e9rieure de Lyon, 46 all\u00e9e d\u2019Italie, 69364 Lyon, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I113428412","https://openalex.org/I100532134","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004658783","display_name":"Birgit Schi\u00f8tt","orcid":"https://orcid.org/0000-0001-9937-1562"},"institutions":[{"id":"https://openalex.org/I204337017","display_name":"Aarhus University","ror":"https://ror.org/01aj84f44","country_code":"DK","type":"education","lineage":["https://openalex.org/I204337017"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Birgit Schi\u00f8tt","raw_affiliation_strings":["Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark","institution_ids":["https://openalex.org/I204337017"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075647448","display_name":"Lorena Zuzic","orcid":"https://orcid.org/0000-0002-7834-612X"},"institutions":[{"id":"https://openalex.org/I204337017","display_name":"Aarhus University","ror":"https://ror.org/01aj84f44","country_code":"DK","type":"education","lineage":["https://openalex.org/I204337017"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Lorena Zuzic","raw_affiliation_strings":["Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark","institution_ids":["https://openalex.org/I204337017"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5075647448"],"corresponding_institution_ids":["https://openalex.org/I204337017"],"apc_list":null,"apc_paid":null,"fwci":4.995,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.95542878,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"65","issue":"10","first_page":"4760","last_page":"4766"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9940000176429749,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.992900013923645,"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/computer-science","display_name":"Computer science","score":0.49458047747612}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49458047747612}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1021/acs.jcim.5c00069","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00069","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40354253","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40354253","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:pure.atira.dk:openaire/bfa237e3-ba48-477b-8869-63701839b444","is_oa":true,"landing_page_url":"https://pure.au.dk/portal/en/publications/bfa237e3-ba48-477b-8869-63701839b444","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Andreasen, M D, Souza, P C T, Schi\u00f8tt, B & Zuzic, L 2025, 'Creating Coarse-Grained Systems with COBY : Toward Higher Accuracy of Complex Biological Systems', Journal of Chemical Information and Modeling, vol. 65, no. 10, pp. 4760-4766. https://doi.org/10.1021/acs.jcim.5c00069","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:HAL:hal-05377341v1","is_oa":true,"landing_page_url":"https://hal.science/hal-05377341","pdf_url":"https://hal.science/hal-05377341/document","source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, 2025, 65 (10), pp.4760-4766. &#x27E8;10.1021/acs.jcim.5c00069&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:12117566","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12117566","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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.5c00069","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00069","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","score":0.6800000071525574,"display_name":"Zero hunger"}],"awards":[{"id":"https://openalex.org/G1936136058","display_name":null,"funder_award_id":"NF20OC0065431","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G3691638365","display_name":null,"funder_award_id":"NNF18OC0032608","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G471403659","display_name":null,"funder_award_id":"346-2020-1944","funder_id":"https://openalex.org/F4320321999","funder_display_name":"Lundbeckfonden"},{"id":"https://openalex.org/G4973929103","display_name":null,"funder_award_id":"funding","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"},{"id":"https://openalex.org/G5640121800","display_name":null,"funder_award_id":"(CNRS)","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"},{"id":"https://openalex.org/G5913983453","display_name":null,"funder_award_id":"AUFF-E-2020-9-1 0","funder_id":"https://openalex.org/F4320321446","funder_display_name":"Aarhus Universitets Forskningsfond"},{"id":"https://openalex.org/G7758152977","display_name":null,"funder_award_id":"support","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"}],"funders":[{"id":"https://openalex.org/F4320307781","display_name":"Sanofi","ror":"https://ror.org/027vj4x92"},{"id":"https://openalex.org/F4320321446","display_name":"Aarhus Universitets Forskningsfond","ror":"https://ror.org/01aj84f44"},{"id":"https://openalex.org/F4320321999","display_name":"Lundbeckfonden","ror":"https://ror.org/03hz8wd80"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"id":"https://openalex.org/F4320327918","display_name":"H. Lundbeck A/S","ror":null},{"id":"https://openalex.org/F4320329934","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W2003949305","https://openalex.org/W2021520922","https://openalex.org/W2058366932","https://openalex.org/W2073268852","https://openalex.org/W2123723715","https://openalex.org/W2149887153","https://openalex.org/W2165097702","https://openalex.org/W2270899054","https://openalex.org/W2321463817","https://openalex.org/W2327174080","https://openalex.org/W2329917942","https://openalex.org/W2460255279","https://openalex.org/W2743526077","https://openalex.org/W2892113269","https://openalex.org/W2910356247","https://openalex.org/W2912735727","https://openalex.org/W3004178265","https://openalex.org/W3006868374","https://openalex.org/W3013142916","https://openalex.org/W3022840618","https://openalex.org/W3048515709","https://openalex.org/W3126435539","https://openalex.org/W3161412790","https://openalex.org/W4205573868","https://openalex.org/W4214530410","https://openalex.org/W4223979303","https://openalex.org/W4226033722","https://openalex.org/W4236442688","https://openalex.org/W4283464776","https://openalex.org/W4310640207","https://openalex.org/W4317433346","https://openalex.org/W4379741281","https://openalex.org/W4380873918","https://openalex.org/W4392231450","https://openalex.org/W4392962544","https://openalex.org/W4394728367"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Current":[0],"trends":[1],"in":[2,16,53,55,74,99,116],"molecular":[3],"modeling":[4],"are":[5,125],"geared":[6],"toward":[7],"increasingly":[8],"realistic":[9],"representations":[10],"of":[11,23,72,83],"the":[12,24,56,84,120],"biological":[13],"environments":[14],"reflected":[15],"larger,":[17],"more":[18],"complex":[19,85],"systems.":[20],"The":[21],"complexity":[22],"system-building":[25],"procedure":[26],"is":[27,41,111],"ideally":[28],"handled":[29],"by":[30],"software":[31,114],"that":[32,51,66],"converts":[33],"user-provided":[34],"descriptors":[35],"into":[36],"system":[37,57,64],"coordinates.":[38],"This,":[39],"however,":[40],"not":[42],"a":[43,62,69,75,100],"trivial":[44],"task,":[45],"as":[46],"building":[47,89,96],"algorithms":[48],"use":[49],"simplifications":[50],"result":[52],"inaccuracies":[54],"properties.":[58],"We":[59],"created":[60],"COBY,":[61],"coarse-grained":[63],"builder":[65],"can":[67],"create":[68],"large":[70],"variety":[71],"systems":[73,98],"single":[76,101],"command":[77],"call":[78],"with":[79],"an":[80,112],"improved":[81],"accuracy":[82],"membrane":[86],"and":[87,103,119,123],"solvent":[88],"procedures.":[90],"COBY":[91,110],"also":[92],"contains":[93],"features":[94],"for":[95],"diverse":[97],"step,":[102],"has":[104],"functionalities":[105],"aiding":[106],"force":[107],"field":[108],"development.":[109],"open-source":[113],"written":[115],"Python":[117],"3,":[118],"code,":[121],"documentation,":[122],"tutorials":[124],"hosted":[126],"at":[127],"https://github.com/MikkelDA/COBY.":[128]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
