{"id":"https://openalex.org/W2911094364","doi":"https://doi.org/10.1371/journal.pcbi.1006649","title":"Ten simple rules on how to create open access and reproducible molecular simulations of biological systems","display_name":"Ten simple rules on how to create open access and reproducible molecular simulations of biological systems","publication_year":2019,"publication_date":"2019-01-17","ids":{"openalex":"https://openalex.org/W2911094364","doi":"https://doi.org/10.1371/journal.pcbi.1006649","mag":"2911094364","pmid":"https://pubmed.ncbi.nlm.nih.gov/30653494"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006649","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006649","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006649&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":"editorial","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.1006649&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072903725","display_name":"Arne Elofsson","orcid":"https://orcid.org/0000-0002-7115-9751"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Arne Elofsson","raw_affiliation_strings":["Department of Biochemistry and Biophysics, Science for life Laboratory, Stockholm University, Solna, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-7115-9751","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Science for life Laboratory, Stockholm University, Solna, Sweden","institution_ids":["https://openalex.org/I161593684","https://openalex.org/I2800139495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050108763","display_name":"Berk Hess","orcid":"https://orcid.org/0000-0002-7498-7763"},"institutions":[{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Berk Hess","raw_affiliation_strings":["Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I86987016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008875190","display_name":"Erik Lindahl","orcid":"https://orcid.org/0000-0002-2734-2794"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Erik Lindahl","raw_affiliation_strings":["Department of Biochemistry and Biophysics, Science for life Laboratory, Stockholm University, Solna, Sweden","Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-2734-2794","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Science for life Laboratory, Stockholm University, Solna, Sweden","institution_ids":["https://openalex.org/I161593684","https://openalex.org/I2800139495"]},{"raw_affiliation_string":"Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I86987016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022075325","display_name":"Alexey V. Onufriev","orcid":"https://orcid.org/0000-0002-4930-6612"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexey Onufriev","raw_affiliation_strings":["Departments of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-4930-6612","affiliations":[{"raw_affiliation_string":"Departments of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia, United States of America","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020854808","display_name":"David van der Spoel","orcid":"https://orcid.org/0000-0002-7659-8526"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"David van der Spoel","raw_affiliation_strings":["Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-7659-8526","affiliations":[{"raw_affiliation_string":"Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679","https://openalex.org/I2800139495"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030271505","display_name":"Anders Wallqvist","orcid":"https://orcid.org/0000-0002-9775-7469"},"institutions":[{"id":"https://openalex.org/I2800986571","display_name":"Telemedicine & Advanced Technology Research Center","ror":"https://ror.org/014pvr265","country_code":"US","type":"other","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2800986571","https://openalex.org/I2802581893"]},{"id":"https://openalex.org/I2802581893","display_name":"United States Army Medical Research and Development Command","ror":"https://ror.org/03cd02q50","country_code":"US","type":"facility","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2802581893"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anders Wallqvist","raw_affiliation_strings":["Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America","institution_ids":["https://openalex.org/I2800986571","https://openalex.org/I2802581893"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5072903725"],"corresponding_institution_ids":["https://openalex.org/I161593684","https://openalex.org/I2800139495"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":null,"has_fulltext":true,"cited_by_count":46,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"15","issue":"1","first_page":"e1006649","last_page":"e1006649"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9994000196456909,"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":0.9994000196456909,"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/T11937","display_name":"Research Data Management Practices","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9789999723434448,"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/simple","display_name":"Simple (philosophy)","score":0.8357990980148315},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6297290325164795}],"concepts":[{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.8357990980148315},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6297290325164795},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D022126","descriptor_name":"Access to Information","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022126","descriptor_name":"Access to Information","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022126","descriptor_name":"Access to Information","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D033181","descriptor_name":"Information Dissemination","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D033181","descriptor_name":"Information Dissemination","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D033181","descriptor_name":"Information Dissemination","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1006649","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006649","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006649&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:30653494","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30653494","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:DiVA.org:uu-377803","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-377803","pdf_url":null,"source":{"id":"https://openalex.org/S4306402042","display_name":"Uppsala University Publications (Uppsala University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123387679","host_organization_name":"Uppsala University","host_organization_lineage":["https://openalex.org/I123387679"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1006649","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006649","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:2c6e294ddf4f46458505a7136b4b5411","is_oa":true,"landing_page_url":"https://doaj.org/article/2c6e294ddf4f46458505a7136b4b5411","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 15, Iss 1, p e1006649 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5336621","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6336246","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006649","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006649","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006649&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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2911094364.pdf","grobid_xml":"https://content.openalex.org/works/W2911094364.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W242446277","https://openalex.org/W2039516744","https://openalex.org/W2041746984","https://openalex.org/W2041902442","https://openalex.org/W2079875740","https://openalex.org/W2090469606","https://openalex.org/W2127377510","https://openalex.org/W2302501749","https://openalex.org/W2413797628","https://openalex.org/W2773787581","https://openalex.org/W2781413279","https://openalex.org/W4250935282","https://openalex.org/W6660870410","https://openalex.org/W6832601715"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W1585007175","https://openalex.org/W2382521049","https://openalex.org/W2390279801","https://openalex.org/W2144385241","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W4253593777"],"abstract_inverted_index":{"All":[0],"PLOS":[1],"journals":[2],"have":[3],"an":[4,31],"open":[5],"data":[6,15],"policy":[7],"that,":[8],"amongst":[9],"other":[10,74],"things,":[11],"states":[12],"that":[13],"all":[14],"and":[16,73],"related":[17],"metadata":[18],"underlying":[19],"the":[20,67],"findings":[21],"reported":[22],"in":[23,30,58],"a":[24],"submitted":[25],"manuscript":[26],"should":[27,43],"be":[28],"deposited":[29],"appropriate":[32],"public":[33],"repository,":[34],"or":[35],"for":[36,66],"smaller":[37],"datasets,":[38],"as":[39,49],"supporting":[40],"information.":[41],"This":[42],"obviously":[44],"apply":[45],"to":[46],"computational":[47],"methods":[48],"well,":[50],"but":[51],"unfortunately":[52],"this":[53],"is":[54,62],"not":[55],"always":[56],"applied":[57],"practice,":[59],"although":[60],"it":[61],"of":[63,70],"greatest":[64],"importance":[65],"scientific":[68],"quality":[69],"simulations":[71],"[1]":[72],"modeling":[75],"projects":[76]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":7}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}