{"id":"https://openalex.org/W3014147611","doi":"https://doi.org/10.1021/acs.jcim.0c00018","title":"Simulation Foundry: Automated and F.A.I.R. Molecular Modeling","display_name":"Simulation Foundry: Automated and F.A.I.R. Molecular Modeling","publication_year":2020,"publication_date":"2020-04-02","ids":{"openalex":"https://openalex.org/W3014147611","doi":"https://doi.org/10.1021/acs.jcim.0c00018","mag":"3014147611","pmid":"https://pubmed.ncbi.nlm.nih.gov/32240586"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00018","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00018","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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045847201","display_name":"Gudrun Gygli","orcid":"https://orcid.org/0000-0001-9119-1778"},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Gudrun Gygli","raw_affiliation_strings":["Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110674827","display_name":"Juergen Pleiss","orcid":null},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Juergen Pleiss","raw_affiliation_strings":["Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1045-8202","affiliations":[{"raw_affiliation_string":"Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5110674827"],"corresponding_institution_ids":["https://openalex.org/I100066346"],"apc_list":null,"apc_paid":null,"fwci":3.7033,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.94295565,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"60","issue":"4","first_page":"1922","last_page":"1927"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9854999780654907,"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":0.7636948227882385},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7132048010826111},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.70257568359375},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.6467469930648804},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.58553147315979},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.5753650665283203},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.5277591347694397},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4665766656398773},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.46606379747390747},{"id":"https://openalex.org/keywords/data-exchange","display_name":"Data exchange","score":0.4559382498264313},{"id":"https://openalex.org/keywords/pooling","display_name":"Pooling","score":0.41962820291519165},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.38852083683013916},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.33086803555488586},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19719266891479492}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7636948227882385},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7132048010826111},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.70257568359375},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.6467469930648804},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.58553147315979},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.5753650665283203},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.5277591347694397},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4665766656398773},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.46606379747390747},{"id":"https://openalex.org/C15845906","wikidata":"https://www.wikidata.org/wiki/Q1172338","display_name":"Data exchange","level":2,"score":0.4559382498264313},{"id":"https://openalex.org/C70437156","wikidata":"https://www.wikidata.org/wiki/Q7228652","display_name":"Pooling","level":2,"score":0.41962820291519165},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.38852083683013916},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.33086803555488586},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19719266891479492},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.0c00018","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00018","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:32240586","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32240586","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G523492319","display_name":null,"funder_award_id":"EXC 310","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7249683039","display_name":null,"funder_award_id":"EXC 2075","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1886944764","https://openalex.org/W1976896799","https://openalex.org/W1978491189","https://openalex.org/W1995808589","https://openalex.org/W2034639274","https://openalex.org/W2036318837","https://openalex.org/W2039516744","https://openalex.org/W2045853185","https://openalex.org/W2081417077","https://openalex.org/W2085962156","https://openalex.org/W2109639235","https://openalex.org/W2115700022","https://openalex.org/W2128031888","https://openalex.org/W2131966673","https://openalex.org/W2150908245","https://openalex.org/W2153580566","https://openalex.org/W2155993193","https://openalex.org/W2169390877","https://openalex.org/W2264374010","https://openalex.org/W2302501749","https://openalex.org/W2321484219","https://openalex.org/W2512087480","https://openalex.org/W2525846441","https://openalex.org/W2540491215","https://openalex.org/W2558342853","https://openalex.org/W2581330672","https://openalex.org/W2584887063","https://openalex.org/W2724683231","https://openalex.org/W2738990641","https://openalex.org/W2764126709","https://openalex.org/W2773787581","https://openalex.org/W2793690814","https://openalex.org/W2802978240","https://openalex.org/W2878993711","https://openalex.org/W2892182810","https://openalex.org/W2895630903","https://openalex.org/W2898119186","https://openalex.org/W2903196289","https://openalex.org/W2912058255","https://openalex.org/W2937207334","https://openalex.org/W2938405458","https://openalex.org/W2941909985","https://openalex.org/W2942491534","https://openalex.org/W2943375675","https://openalex.org/W2943833343","https://openalex.org/W2947749359","https://openalex.org/W2952026168","https://openalex.org/W2967780898","https://openalex.org/W2972537665","https://openalex.org/W2972663447","https://openalex.org/W2972751083","https://openalex.org/W2974666250","https://openalex.org/W2979538819","https://openalex.org/W2980011270","https://openalex.org/W2995663905","https://openalex.org/W3097977069","https://openalex.org/W3122702518"],"related_works":["https://openalex.org/W3023169329","https://openalex.org/W4389470870","https://openalex.org/W2782165897","https://openalex.org/W1582950852","https://openalex.org/W4300438041","https://openalex.org/W2054104202","https://openalex.org/W2139703748","https://openalex.org/W2761254753","https://openalex.org/W1024825291","https://openalex.org/W2188981919"],"abstract_inverted_index":{"The":[0,35,48,96,117,147,178],"Simulation":[1],"Foundry":[2],"(SF)":[3],"is":[4,122,194],"a":[5,51,151,181],"modular":[6],"workflow":[7],"for":[8,19,60],"the":[9,20,24,71,85,120,138,156,167,170],"automated":[10],"creation":[11],"of":[12,23,29,108,119,126,129,140,154,169],"molecular":[13,114],"modeling":[14],"(MM)":[15],"data.":[16],"MM":[17,38,86],"allows":[18],"reliable":[21],"prediction":[22],"microscopic":[25],"and":[26,41,45,55,65,90,94,173,176,190,196],"macroscopic":[27],"properties":[28,128],"multicomponent":[30,109],"systems":[31,110],"from":[32,145],"first":[33],"principles.":[34],"SF":[36,49,72,97,121,148,179],"makes":[37],"repeatable,":[39],"replicable,":[40],"findable,":[42],"accessible,":[43],"interoperable,":[44],"reusable":[46,93],"(F.A.I.R.).":[47],"uses":[50],"standardized":[52,133],"data":[53,134,142,144,192],"structure":[54],"file":[56],"naming":[57],"convention,":[58],"allowing":[59],"replication":[61],"on":[62,69,77,184],"different":[63],"supercomputers":[64],"re-entrancy.":[66],"We":[67],"focus":[68],"keeping":[70],"simple":[73],"by":[74,84,111,124],"basing":[75],"it":[76,92],"scripting":[78],"languages":[79],"that":[80,193],"are":[81],"widely":[82],"used":[83],"community":[87,182],"(bash,":[88],"Python)":[89],"making":[91],"re-editable.":[95],"was":[98],"developed":[99],"to":[100,186],"assist":[101],"expert":[102],"users":[103],"in":[104],"performing":[105],"parameter":[106],"studies":[107],"high":[112],"throughput":[113],"dynamics":[115],"simulations.":[116],"usability":[118],"demonstrated":[123],"simulations":[125],"thermophysical":[127],"binary":[130],"mixtures.":[131],"A":[132],"exchange":[135],"format":[136],"enables":[137],"integration":[139],"simulated":[141],"with":[143],"experiments.":[146],"also":[149],"provides":[150,180],"complete":[152],"documentation":[153],"how":[155],"results":[157],"were":[158],"obtained,":[159],"thus":[160],"assigning":[161],"provenance.":[162],"Increasing":[163],"computational":[164],"power":[165],"facilitates":[166],"intensification":[168],"simulation":[171],"process":[172],"requires":[174],"automation":[175],"modularity.":[177],"platform":[183],"which":[185],"integrate":[187],"new":[188],"methods":[189],"create":[191],"reproducible":[195],"transparent":[197],"(https://fairdomhub.org/studies/639/snapshots/1,":[198],"https://fairdomhub.org/studies/639/snapshots/2).":[199]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
