{"id":"https://openalex.org/W2037431084","doi":"https://doi.org/10.1021/ci500173w","title":"iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings","display_name":"iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings","publication_year":2014,"publication_date":"2014-05-15","ids":{"openalex":"https://openalex.org/W2037431084","doi":"https://doi.org/10.1021/ci500173w","mag":"2037431084","pmid":"https://pubmed.ncbi.nlm.nih.gov/24830957"},"language":"en","primary_location":{"id":"doi:10.1021/ci500173w","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci500173w","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":"publisher-specific-oa","license_id":"https://openalex.org/licenses/publisher-specific-oa","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/A5110202807","display_name":"Julien Thibault","orcid":null},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Julien C. Thibault","raw_affiliation_strings":["Department of Biomedical\rInformatics and \u2021Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical\rInformatics and \u2021Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020579549","display_name":"Thomas E. Cheatham","orcid":"https://orcid.org/0000-0003-0298-3904"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas E. Cheatham","raw_affiliation_strings":["Department of Biomedical\rInformatics and \u2021Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical\rInformatics and \u2021Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007190695","display_name":"Julio C. Facelli","orcid":"https://orcid.org/0000-0003-1449-477X"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julio C. Facelli","raw_affiliation_strings":["Department of Biomedical\rInformatics and \u2021Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical\rInformatics and \u2021Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States","institution_ids":["https://openalex.org/I223532165"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5110202807"],"corresponding_institution_ids":["https://openalex.org/I223532165"],"apc_list":null,"apc_paid":null,"fwci":2.6127,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.92428174,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"54","issue":"6","first_page":"1810","last_page":"1819"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9922999739646912,"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":0.9922999739646912,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9921000003814697,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9873999953269958,"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":0.8836942911148071},{"id":"https://openalex.org/keywords/automatic-summarization","display_name":"Automatic summarization","score":0.5711565613746643},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.5625578761100769},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5354623198509216},{"id":"https://openalex.org/keywords/html","display_name":"HTML","score":0.5312554240226746},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.4817062020301819},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.46650901436805725},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.44046786427497864},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.42842185497283936},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4109065532684326},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3852894902229309},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.27667027711868286},{"id":"https://openalex.org/keywords/web-page","display_name":"Web page","score":0.1979818046092987}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8836942911148071},{"id":"https://openalex.org/C170858558","wikidata":"https://www.wikidata.org/wiki/Q1394144","display_name":"Automatic summarization","level":2,"score":0.5711565613746643},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.5625578761100769},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5354623198509216},{"id":"https://openalex.org/C138708601","wikidata":"https://www.wikidata.org/wiki/Q8811","display_name":"HTML","level":3,"score":0.5312554240226746},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.4817062020301819},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.46650901436805725},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.44046786427497864},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.42842185497283936},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4109065532684326},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3852894902229309},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.27667027711868286},{"id":"https://openalex.org/C21959979","wikidata":"https://www.wikidata.org/wiki/Q36774","display_name":"Web page","level":2,"score":0.1979818046092987},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci500173w","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci500173w","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":"publisher-specific-oa","license_id":"https://openalex.org/licenses/publisher-specific-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:24830957","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24830957","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:europepmc.org:3398931","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4076027","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1690346126","display_name":null,"funder_award_id":"CHE-1266307","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5432939948","display_name":null,"funder_award_id":"R01-GM081411","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1965092590","https://openalex.org/W1989383586","https://openalex.org/W2016088798","https://openalex.org/W2026020661","https://openalex.org/W2054652150","https://openalex.org/W2081417077","https://openalex.org/W2118233996","https://openalex.org/W2124357718","https://openalex.org/W2128031888","https://openalex.org/W2137726543","https://openalex.org/W2150981663","https://openalex.org/W2160544821"],"related_works":["https://openalex.org/W4385386698","https://openalex.org/W2042562985","https://openalex.org/W4235354490","https://openalex.org/W183683573","https://openalex.org/W2143258726","https://openalex.org/W2381082207","https://openalex.org/W2025266532","https://openalex.org/W2136793911","https://openalex.org/W1971521465","https://openalex.org/W2377737135"],"abstract_inverted_index":{"As":[0],"the":[1,23,68,84,109,130],"amount":[2],"of":[3,51],"data":[4,21,44,93,96,115,156,179],"generated":[5,158],"by":[6],"biomolecular":[7,42],"simulations":[8],"dramatically":[9],"increases,":[10],"new":[11],"tools":[12],"need":[13],"to":[14,17,55,60,77,86],"be":[15],"developed":[16],"help":[18],"manage":[19],"this":[20,32],"at":[22,149,186],"individual":[24],"investigator":[25],"or":[26],"small":[27],"research":[28],"group":[29],"level.":[30],"In":[31],"paper,":[33],"we":[34],"introduce":[35],"iBIOMES":[36,52,141],"Lite,":[37],"a":[38,57,65],"lightweight":[39],"tool":[40],"for":[41],"simulation":[43,92,110],"indexing":[45],"and":[46,74,89,112,148,161,167,177],"summarization.":[47],"The":[48,118,169,182],"main":[49],"goal":[50],"Lite":[53,142],"is":[54,121,134,184],"provide":[56],"simple":[58],"interface":[59,82],"summarize":[61,108],"computational":[62],"experiments":[63],"in":[64],"setting":[66],"where":[67],"user":[69,85],"might":[70],"have":[71],"limited":[72,75],"privileges":[73],"access":[76],"IT":[78],"resources.":[79],"A":[80],"command-line":[81],"allows":[83],"summarize,":[87],"publish,":[88],"search":[90],"local":[91],"sets.":[94],"Published":[95],"sets":[97,157],"are":[98],"accessible":[99],"via":[100,123],"static":[101],"hypertext":[102],"markup":[103,125],"language":[104,126,139],"(HTML)":[105],"pages":[106],"that":[107],"protocols":[111],"also":[113],"display":[114],"analysis":[116],"graphically.":[117],"publication":[119],"process":[120],"customized":[122,135],"extensible":[124,137],"(XML)":[127],"descriptors":[128],"while":[129],"HTML":[131],"summary":[132],"template":[133],"through":[136,159],"stylesheet":[138],"(XSL).":[140],"was":[143],"tested":[144],"on":[145],"different":[146],"platforms":[147],"several":[150],"national":[151],"computing":[152],"centers":[153],"using":[154],"various":[155],"classical":[160],"quantum":[162,165],"molecular":[163],"dynamics,":[164],"chemistry,":[166],"QM/MM.":[168],"associated":[170],"parsers":[171],"currently":[172],"support":[173],"AMBER,":[174],"GROMACS,":[175],"Gaussian,":[176],"NWChem":[178],"set":[180],"publication.":[181],"code":[183],"available":[185],"https://github.com/jcvthibault/ibiomes":[187],".":[188]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
