{"id":"https://openalex.org/W2971540143","doi":"https://doi.org/10.1021/acs.jcim.9b00252","title":"TMB Library of Nucleosome Simulations","display_name":"TMB Library of Nucleosome Simulations","publication_year":2019,"publication_date":"2019-09-06","ids":{"openalex":"https://openalex.org/W2971540143","doi":"https://doi.org/10.1021/acs.jcim.9b00252","mag":"2971540143","pmid":"https://pubmed.ncbi.nlm.nih.gov/31490686"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00252","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00252","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/A5090934539","display_name":"Ran Sun","orcid":"https://orcid.org/0000-0001-9326-9313"},"institutions":[{"id":"https://openalex.org/I919208787","display_name":"Louisiana Tech University","ror":"https://ror.org/04q9esz89","country_code":"US","type":"education","lineage":["https://openalex.org/I2799628689","https://openalex.org/I919208787"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ran Sun","raw_affiliation_strings":["College of Engineering and Science \u00a0and\u00a0 Engineering Physics Program, Louisiana Tech University, Ruston, Louisiana 71272, United States"],"raw_orcid":"https://orcid.org/0000-0001-9326-9313","affiliations":[{"raw_affiliation_string":"College of Engineering and Science \u00a0and\u00a0 Engineering Physics Program, Louisiana Tech University, Ruston, Louisiana 71272, United States","institution_ids":["https://openalex.org/I919208787"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100699762","display_name":"Zilong Li","orcid":"https://orcid.org/0000-0002-5134-7026"},"institutions":[{"id":"https://openalex.org/I919208787","display_name":"Louisiana Tech University","ror":"https://ror.org/04q9esz89","country_code":"US","type":"education","lineage":["https://openalex.org/I2799628689","https://openalex.org/I919208787"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zilong Li","raw_affiliation_strings":["College of Engineering and Science \u00a0and\u00a0 Computational Analysis and Modeling Program, Louisiana Tech University, Ruston, Louisiana 71272, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Engineering and Science \u00a0and\u00a0 Computational Analysis and Modeling Program, Louisiana Tech University, Ruston, Louisiana 71272, United States","institution_ids":["https://openalex.org/I919208787"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003492695","display_name":"Thomas C. Bishop","orcid":"https://orcid.org/0000-0003-4264-4261"},"institutions":[{"id":"https://openalex.org/I919208787","display_name":"Louisiana Tech University","ror":"https://ror.org/04q9esz89","country_code":"US","type":"education","lineage":["https://openalex.org/I2799628689","https://openalex.org/I919208787"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Thomas C. Bishop","raw_affiliation_strings":["College of Engineering and Science \u00a0and\u00a0 Chemistry and Physics Programs, Louisiana Tech University, Ruston, Louisiana 71272, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Engineering and Science \u00a0and\u00a0 Chemistry and Physics Programs, Louisiana Tech University, Ruston, Louisiana 71272, United States","institution_ids":["https://openalex.org/I919208787"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003492695"],"corresponding_institution_ids":["https://openalex.org/I919208787"],"apc_list":null,"apc_paid":null,"fwci":0.859,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.73136251,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"59","issue":"10","first_page":"4289","last_page":"4299"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9995999932289124,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991000294685364,"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/nucleosome","display_name":"Nucleosome","score":0.9383940100669861},{"id":"https://openalex.org/keywords/superhelix","display_name":"Superhelix","score":0.9157460927963257},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.6057767271995544},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6013999581336975},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5867601037025452},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4590604901313782},{"id":"https://openalex.org/keywords/linker-dna","display_name":"Linker DNA","score":0.4382554590702057},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.4269223213195801},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40004050731658936},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.39804285764694214},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3900303840637207},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36780256032943726},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29257380962371826},{"id":"https://openalex.org/keywords/dna-supercoil","display_name":"DNA supercoil","score":0.21127262711524963},{"id":"https://openalex.org/keywords/dna-replication","display_name":"DNA replication","score":0.1833314597606659}],"concepts":[{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.9383940100669861},{"id":"https://openalex.org/C2779408652","wikidata":"https://www.wikidata.org/wiki/Q7643415","display_name":"Superhelix","level":5,"score":0.9157460927963257},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.6057767271995544},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6013999581336975},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5867601037025452},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4590604901313782},{"id":"https://openalex.org/C193646685","wikidata":"https://www.wikidata.org/wiki/Q1826830","display_name":"Linker DNA","level":5,"score":0.4382554590702057},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.4269223213195801},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40004050731658936},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.39804285764694214},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3900303840637207},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36780256032943726},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29257380962371826},{"id":"https://openalex.org/C158456008","wikidata":"https://www.wikidata.org/wiki/Q412639","display_name":"DNA supercoil","level":4,"score":0.21127262711524963},{"id":"https://openalex.org/C73573662","wikidata":"https://www.wikidata.org/wiki/Q130996","display_name":"DNA replication","level":3,"score":0.1833314597606659}],"mesh":[{"descriptor_ui":"D000080911","descriptor_name":"Cheminformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000080911","descriptor_name":"Cheminformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000080911","descriptor_name":"Cheminformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000080911","descriptor_name":"Cheminformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000080911","descriptor_name":"Cheminformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","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},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b00252","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00252","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:31490686","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31490686","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/G1213398505","display_name":null,"funder_award_id":"OIA-1541079","funder_id":"https://openalex.org/F4320337378","funder_display_name":"Office of Integrative Activities"},{"id":"https://openalex.org/G8535401761","display_name":null,"funder_award_id":"P20 GM103424-17","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337378","display_name":"Office of Integrative Activities","ror":"https://ror.org/04k9mqs78"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1584891530","https://openalex.org/W1969934670","https://openalex.org/W1976499671","https://openalex.org/W1980722147","https://openalex.org/W1988997227","https://openalex.org/W2004206635","https://openalex.org/W2006056178","https://openalex.org/W2022288592","https://openalex.org/W2023621898","https://openalex.org/W2030618860","https://openalex.org/W2032820551","https://openalex.org/W2035266068","https://openalex.org/W2036031364","https://openalex.org/W2037431084","https://openalex.org/W2039227903","https://openalex.org/W2049475242","https://openalex.org/W2054669424","https://openalex.org/W2059745208","https://openalex.org/W2067174909","https://openalex.org/W2069545688","https://openalex.org/W2073240448","https://openalex.org/W2075802914","https://openalex.org/W2076446466","https://openalex.org/W2081417077","https://openalex.org/W2081725132","https://openalex.org/W2092006003","https://openalex.org/W2097585916","https://openalex.org/W2100380699","https://openalex.org/W2108669081","https://openalex.org/W2118526609","https://openalex.org/W2128031888","https://openalex.org/W2135184237","https://openalex.org/W2137726543","https://openalex.org/W2144288821","https://openalex.org/W2150945052","https://openalex.org/W2150981663","https://openalex.org/W2151553287","https://openalex.org/W2151991601","https://openalex.org/W2152605077","https://openalex.org/W2154456026","https://openalex.org/W2157089275","https://openalex.org/W2174058075","https://openalex.org/W2263010949","https://openalex.org/W2317758137","https://openalex.org/W2344252179","https://openalex.org/W2404280981","https://openalex.org/W2483384142","https://openalex.org/W2503031483","https://openalex.org/W2728165287","https://openalex.org/W2796205786","https://openalex.org/W2901756091","https://openalex.org/W2903457010","https://openalex.org/W2905031578","https://openalex.org/W4301038299"],"related_works":["https://openalex.org/W2062514148","https://openalex.org/W2583501156","https://openalex.org/W2073240448","https://openalex.org/W1979629335","https://openalex.org/W2063259914","https://openalex.org/W2010793324","https://openalex.org/W1602926270","https://openalex.org/W1998677442","https://openalex.org/W2323586011","https://openalex.org/W2614589724"],"abstract_inverted_index":{"oligonucleotides":[0],"that":[1],"can":[2,211,248],"form":[3],"a":[4,24,48,58,64,68,89,93,116,223],"nucleosome.":[5,42],"Comparative,":[6],"rather":[7],"than":[8,140],"comprehensive,":[9],"studies":[10,228],"are":[11,83,160],"required.":[12],"Here":[13],"we":[14],"introduce":[15],"the":[16,41,108,121,146,163,181,186,192,204,220,236],"TMB":[17,44,109,246],"Library":[18,45,247],"of":[19,26,30,40,55,60,100,107,123,148,158,165,168,177,188,197,203,229,235,238],"nucleosome":[20,182,208],"simulations":[21,35,54,157,216],"and":[22,57,78,92,129,183,195,201,231,240],"present":[23],"meta-analysis":[25,106],"over":[27],"20":[28],"\u03bcs":[29],"all":[31],"atom":[32],"molecular":[33],"dynamics":[34,196],"representing":[36],"518":[37],"different":[38],"realizations":[39],"The":[43,173,245],"serves":[46],"as":[47,63],"reference":[49],"for":[50,66,126,225],"future":[51],"comparative,":[52],"on-demand":[53],"nucleosomes":[56,159,230],"demonstration":[59],"iBIOMES":[61,86],"Lite":[62,87],"tool":[65],"managing":[67],"laboratory's":[69],"simulation":[70,227],"library.":[71],"For":[72],"every":[73],"simulation,":[74],"dewatered":[75],"trajectories,":[76],"RMSD,":[77],"DNA":[79,102,111,141,151,169,178,189],"helical":[80,152],"parameter":[81,153],"data":[82],"provided":[84],"through":[85],"in":[88,143,171,180,214],"Web":[90],"browser":[91,95],"file":[94],"format.":[96],"A":[97],"novel":[98],"view":[99],"nucleosomal":[101,243],"emerges":[103],"from":[104,156],"our":[105,233],"Library.":[110],"conformation":[112],"is":[113,132],"restricted":[114,135],"to":[115,242],"specific":[117],"left-handed":[118],"superhelix,":[119],"but":[120],"range":[122,164],"conformations":[124],"observed":[125],"individual":[127],"bases":[128],"base":[130],"pairs":[131],"not":[133],"more":[134,137],"nor":[136],"highly":[138],"deformed":[139],"free":[142,170],"solution.":[144,172],"With":[145],"exception":[147],"Roll,":[149],"mean":[150],"values":[154],"obtained":[155],"largely":[161],"within":[162],"thermal":[166],"motion":[167],"library":[174],"provides":[175],"evidence":[176],"kinking":[179],"clearly":[184],"demonstrates":[185],"effects":[187,200],"sequence":[190,210],"on":[191],"gross":[193],"structure":[194],"nucleosomes.":[198],"These":[199],"mispositioning":[202],"601":[205],"super":[206],"strong":[207],"positioning":[209],"be":[212,249],"detected":[213],"short":[215],"(10":[217],"ns).":[218],"Collectively,":[219],"results":[221],"provide":[222],"basis":[224],"comparative":[226],"extend":[232],"understanding":[234],"binding":[237],"proteins":[239],"drugs":[241],"DNA.":[244],"found":[250],"at":[251],"http://dna.engr.latech.edu/~tmbshare/":[252],".":[253]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}