{"id":"https://openalex.org/W4407783312","doi":"https://doi.org/10.1021/acs.jcim.4c01301","title":"A FAIR-Compliant Management Solution for Molecular Simulation Trajectories","display_name":"A FAIR-Compliant Management Solution for Molecular Simulation Trajectories","publication_year":2025,"publication_date":"2025-02-20","ids":{"openalex":"https://openalex.org/W4407783312","doi":"https://doi.org/10.1021/acs.jcim.4c01301","pmid":"https://pubmed.ncbi.nlm.nih.gov/39977657"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01301","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01301","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.4c01301","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024363437","display_name":"Andreas Vitalis","orcid":"https://orcid.org/0000-0002-5422-5278"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Andreas Vitalis","raw_affiliation_strings":["Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-5422-5278","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116346423","display_name":"Steffen Winkler","orcid":"https://orcid.org/0000-0003-0919-6356"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Steffen Winkler","raw_affiliation_strings":["Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-0919-6356","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125123000","display_name":"Yang Zhang","orcid":"https://orcid.org/0000-0003-0801-8064"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Yang Zhang","raw_affiliation_strings":["Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-0801-8064","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091989880","display_name":"Julian Widmer","orcid":"https://orcid.org/0009-0006-7025-7364"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Julian Widmer","raw_affiliation_strings":["Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035048768","display_name":"Amedeo Caflisch","orcid":"https://orcid.org/0000-0002-2317-6792"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Amedeo Caflisch","raw_affiliation_strings":["Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-2317-6792","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5024363437"],"corresponding_institution_ids":["https://openalex.org/I202697423"],"apc_list":null,"apc_paid":null,"fwci":7.3143,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.95961366,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"65","issue":"5","first_page":"2443","last_page":"2455"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9988999962806702,"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":0.9988999962806702,"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":0.9839000105857849,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.975600004196167,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4644510746002197}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4644510746002197}],"mesh":[{"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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"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":"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:10.1021/acs.jcim.4c01301","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01301","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:39977657","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39977657","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:doi:10.5167/uzh-275838","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11898051","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11898051","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":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c01301","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01301","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":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":69,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1542579814","https://openalex.org/W1966041739","https://openalex.org/W1970022221","https://openalex.org/W1970897635","https://openalex.org/W1975734016","https://openalex.org/W1984493861","https://openalex.org/W1995808589","https://openalex.org/W1997108831","https://openalex.org/W1997772366","https://openalex.org/W2003213558","https://openalex.org/W2010005232","https://openalex.org/W2012616517","https://openalex.org/W2016267980","https://openalex.org/W2022288592","https://openalex.org/W2028263411","https://openalex.org/W2029667189","https://openalex.org/W2040809566","https://openalex.org/W2041902442","https://openalex.org/W2057477511","https://openalex.org/W2067236515","https://openalex.org/W2075460992","https://openalex.org/W2088107354","https://openalex.org/W2099211347","https://openalex.org/W2103945336","https://openalex.org/W2106140689","https://openalex.org/W2117897850","https://openalex.org/W2128572087","https://openalex.org/W2132629607","https://openalex.org/W2140047797","https://openalex.org/W2150662472","https://openalex.org/W2161134038","https://openalex.org/W2162166182","https://openalex.org/W2174058075","https://openalex.org/W2302501749","https://openalex.org/W2319902168","https://openalex.org/W2336883206","https://openalex.org/W2410114406","https://openalex.org/W2422799170","https://openalex.org/W2724683231","https://openalex.org/W2804174632","https://openalex.org/W2892113269","https://openalex.org/W2896638470","https://openalex.org/W2913743073","https://openalex.org/W2964011450","https://openalex.org/W3010340553","https://openalex.org/W3042198040","https://openalex.org/W3083778208","https://openalex.org/W3083979690","https://openalex.org/W3097781375","https://openalex.org/W3113859666","https://openalex.org/W3135534391","https://openalex.org/W3183869552","https://openalex.org/W4229029935","https://openalex.org/W4255584963","https://openalex.org/W4281666052","https://openalex.org/W4309160459","https://openalex.org/W4361291818","https://openalex.org/W4376128736","https://openalex.org/W4376642773","https://openalex.org/W4385564481","https://openalex.org/W4388638767","https://openalex.org/W4388870515","https://openalex.org/W4392293365","https://openalex.org/W4396695310","https://openalex.org/W4396789292","https://openalex.org/W4401102549","https://openalex.org/W4402063381","https://openalex.org/W4404328867"],"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":{"Simulation":[0],"studies":[1,110],"of":[2,11,17,24,28,46,70,82,85,93,122,165,181,199,216,223],"molecules":[3,84],"primarily":[4],"produce":[5],"data":[6,123,219],"that":[7,128,151,195],"represent":[8],"the":[9,12,18,25,47,57,66,71,78,83,120,132,166,179,213],"configuration":[10],"system":[13],"as":[14],"a":[15,44,61,117,142,162,196,207,226],"function":[16],"progress":[19],"variable,":[20],"usually":[21],"time.":[22],"Because":[23],"high-dimensional":[26],"nature":[27],"these":[29,173],"data,":[30,159,201],"which":[31,160],"grow":[32],"very":[33],"quickly,":[34],"compromises":[35],"are":[36],"often":[37],"necessary":[38],"and":[39,54,111,137,157,225],"achieved":[40],"by":[41,55,125],"storing":[42,172],"only":[43,96],"subset":[45],"system's":[48],"components,":[49],"for":[50,108,119,171,178,229],"example,":[51],"stripping":[52],"solvent,":[53],"restricting":[56],"time":[58,68],"resolution":[59],"to":[60,206],"scale":[62],"significantly":[63],"coarser":[64],"than":[65],"basic":[67],"step":[69],"simulation.":[72],"The":[73],"resultant":[74],"trajectories":[75],"thus":[76],"describe":[77,141],"essentially":[79],"stochastic":[80],"evolution":[81],"interest.":[86],"Maintaining":[87],"their":[88],"interpretability":[89],"through":[90],"metadata":[91,156],"is":[92,161,184,232],"interest":[94],"not":[95],"because":[97],"they":[98],"can":[99,211],"aid":[100],"researchers":[101],"interested":[102],"in":[103,145,202],"specific":[104],"systems":[105],"but":[106],"also":[107],"reproducibility":[109],"model":[112],"refinement.":[113],"Here,":[114],"we":[115,193],"introduce":[116],"standard":[118],"storage":[121,198],"created":[124],"molecular":[126,217],"simulations":[127],"improves":[129],"compliance":[130,215],"with":[131,148,187],"FAIR":[133,214],"(Findable,":[134],"Accessible,":[135],"Interoperable,":[136],"Reusable)":[138],"principles.":[139],"We":[140],"solution":[143,228],"conceived":[144],"PostgreSQL,":[146],"along":[147,186],"reference":[149],"implementations,":[150],"provides":[152],"stringent":[153],"links":[154],"between":[155],"raw":[158],"major":[163],"weakness":[164],"established":[167],"file":[168],"formats":[169],"used":[170],"data.":[174],"A":[175],"possible":[176],"structure":[177],"logic":[180],"SQL":[182],"queries":[183],"included":[185],"salient":[188],"performance":[189],"testing.":[190],"To":[191],"close,":[192],"suggest":[194],"PostgreSQL-based":[197],"simulation":[200,218],"particular":[203],"when":[204],"coupled":[205],"visual":[208],"user":[209],"interface,":[210],"improve":[212],"at":[220],"all":[221],"levels":[222],"visibility,":[224],"prototype":[227],"accomplishing":[230],"this":[231],"presented.":[233]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
