{"id":"https://openalex.org/W4361250337","doi":"https://doi.org/10.1021/acs.jcim.3c00250","title":"Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide","display_name":"Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide","publication_year":2023,"publication_date":"2023-03-30","ids":{"openalex":"https://openalex.org/W4361250337","doi":"https://doi.org/10.1021/acs.jcim.3c00250","pmid":"https://pubmed.ncbi.nlm.nih.gov/36996447"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00250","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00250","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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.3c00250","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037022759","display_name":"Lauren Winkler","orcid":"https://orcid.org/0000-0002-9439-3225"},"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":"Lauren Winkler","raw_affiliation_strings":["Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"last","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":true,"raw_author_name":"Thomas E. Cheatham","raw_affiliation_strings":["Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States","institution_ids":["https://openalex.org/I223532165"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5020579549"],"corresponding_institution_ids":["https://openalex.org/I223532165"],"apc_list":null,"apc_paid":null,"fwci":2.2103,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.8754706,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"63","issue":"8","first_page":"2505","last_page":"2511"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9997000098228455,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9997000098228455,"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":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9983999729156494,"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/polarizability","display_name":"Polarizability","score":0.9007411599159241},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.8213384747505188},{"id":"https://openalex.org/keywords/drude-model","display_name":"Drude model","score":0.6570853590965271},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.5663605332374573},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5583067536354065},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5100106000900269},{"id":"https://openalex.org/keywords/stacking","display_name":"Stacking","score":0.4442523121833801},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4236191511154175},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.41274142265319824},{"id":"https://openalex.org/keywords/biomolecule","display_name":"Biomolecule","score":0.4127236306667328},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.38367289304733276},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.35245707631111145},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.28073152899742126},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.22470420598983765},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.22167879343032837},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.1598118245601654},{"id":"https://openalex.org/keywords/nuclear-magnetic-resonance","display_name":"Nuclear magnetic resonance","score":0.12503081560134888}],"concepts":[{"id":"https://openalex.org/C139287275","wikidata":"https://www.wikidata.org/wiki/Q869891","display_name":"Polarizability","level":3,"score":0.9007411599159241},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.8213384747505188},{"id":"https://openalex.org/C2776445377","wikidata":"https://www.wikidata.org/wiki/Q910043","display_name":"Drude model","level":2,"score":0.6570853590965271},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.5663605332374573},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5583067536354065},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5100106000900269},{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.4442523121833801},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4236191511154175},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.41274142265319824},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.4127236306667328},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.38367289304733276},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.35245707631111145},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.28073152899742126},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.22470420598983765},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.22167879343032837},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.1598118245601654},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.12503081560134888},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","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":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.3c00250","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00250","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:36996447","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36996447","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:pubmedcentral.nih.gov:10131218","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10131218","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10131218/pdf/ci3c00250.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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.3c00250","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00250","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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":[{"id":"https://openalex.org/G4022133507","display_name":null,"funder_award_id":"R-01 GM-081411","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1930867640","https://openalex.org/W1952317074","https://openalex.org/W1976499671","https://openalex.org/W1983814953","https://openalex.org/W1989383586","https://openalex.org/W2001069120","https://openalex.org/W2004640547","https://openalex.org/W2010471143","https://openalex.org/W2021032453","https://openalex.org/W2021520922","https://openalex.org/W2035956399","https://openalex.org/W2038354555","https://openalex.org/W2043782165","https://openalex.org/W2052329232","https://openalex.org/W2057653269","https://openalex.org/W2061029954","https://openalex.org/W2108538233","https://openalex.org/W2116413427","https://openalex.org/W2132262459","https://openalex.org/W2170595734","https://openalex.org/W2171047927","https://openalex.org/W2332270957","https://openalex.org/W2337762266","https://openalex.org/W2439052303","https://openalex.org/W2439564735","https://openalex.org/W2523240039","https://openalex.org/W2563104535","https://openalex.org/W2605759800","https://openalex.org/W2607390045","https://openalex.org/W2782369838","https://openalex.org/W2899110998","https://openalex.org/W2902642334","https://openalex.org/W2949223833","https://openalex.org/W3105272336","https://openalex.org/W3192722868","https://openalex.org/W3217676662","https://openalex.org/W4200524940"],"related_works":["https://openalex.org/W2169925204","https://openalex.org/W2035329725","https://openalex.org/W2150263332","https://openalex.org/W3154110438","https://openalex.org/W2022139008","https://openalex.org/W4240765804","https://openalex.org/W2056177562","https://openalex.org/W2038920006","https://openalex.org/W4321018347","https://openalex.org/W4361250337"],"abstract_inverted_index":{"Polarizable":[0],"force":[1,8,56,162,178],"fields,":[2],"in":[3,37,122,158],"particular,":[4],"the":[5,14,53,71,88,94,100,109,117,129,159,171,175,185],"Drude":[6,54,160,176],"polarizable":[7,55,161,177],"field":[9,57,163,179],"(Drude":[10],"FF),":[11],"may":[12],"hold":[13],"key":[15],"to":[16,65,183,191],"more":[17],"accurately":[18,192],"modeling":[19],"biomolecules":[20],"with":[21,45,48,58,82,128],"molecular":[22],"dynamics":[23],"simulations":[24],"by":[25],"explicitly":[26],"accounting":[27],"for":[28,146],"atomic":[29],"polarizability.":[30],"Previous":[31],"work":[32],"has":[33,63],"shown":[34],"promising":[35],"results":[36],"simulating":[38],"duplex":[39],"nucleic":[40],"acids":[41],"and":[42,132,136],"protein":[43],"structures":[44,62,124,143],"excellent":[46],"agreement":[47],"experimental":[49,101],"values.":[50],"However,":[51],"benchmarking":[52],"highly":[59],"flexible,":[60],"single-stranded":[61,195],"yet":[64],"be":[66],"achieved.":[67],"In":[68,107],"this":[69],"work,":[70],"r(GACC)":[72,118],"tetranucleotide":[73,119],"is":[74,104,113,168],"simulated":[75],"over":[76,139],"a":[77,154],"multimicrosecond":[78],"time":[79,148],"scale,":[80],"starting":[81,89,92],"various":[83],"different":[84],"initial":[85],"conformations.":[86],"Despite":[87],"conformation,":[90,99],"including":[91],"from":[93],"expected":[95],"dominant":[96],"A-form":[97],"major":[98,110],"structural":[102],"distribution":[103],"not":[105,181],"matched.":[106],"fact,":[108],"NMR":[111,130],"conformation":[112],"never":[114],"resampled.":[115],"Instead,":[116],"becomes":[120],"stabilized":[121],"anomalous":[123],"that":[125,133,173],"are":[126,144],"inconsistent":[127],"data":[131],"favor":[134],"base-pairing":[135],"electrostatic":[137],"interactions":[138],"base":[140],"stacking.":[141],"These":[142],"maintained":[145],"lengthy":[147],"scales":[149],"(>1":[150],"\u03bcs)":[151],"themselves,":[152],"suggesting":[153],"misbalance":[155],"of":[156,170,188],"forces":[157,189],"itself.":[164],"This":[165],"model":[166,193],"system":[167],"suggestive":[169],"fact":[172],"currently":[174],"does":[180],"appear":[182],"produce":[184],"sensitive":[186],"balance":[187],"required":[190],"other":[194],"or":[196],"noncanonical":[197],"RNA":[198],"structures.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":6}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}