{"id":"https://openalex.org/W2561780902","doi":"https://doi.org/10.1021/acs.jcim.6b00660","title":"Biasing Simulations of DNA Base Pair Parameters with Application to Propellor Twisting in AT/AT, AA/TT, and AC/GT Steps and Their Uracil Analogs","display_name":"Biasing Simulations of DNA Base Pair Parameters with Application to Propellor Twisting in AT/AT, AA/TT, and AC/GT Steps and Their Uracil Analogs","publication_year":2016,"publication_date":"2016-12-15","ids":{"openalex":"https://openalex.org/W2561780902","doi":"https://doi.org/10.1021/acs.jcim.6b00660","mag":"2561780902","pmid":"https://pubmed.ncbi.nlm.nih.gov/27976883"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00660","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00660","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/A5047241220","display_name":"Alfredo Peguero\u2010Tejada","orcid":null},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alfredo Peguero-Tejada","raw_affiliation_strings":["Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States","institution_ids":["https://openalex.org/I2613432"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012698288","display_name":"Arjan van der Vaart","orcid":"https://orcid.org/0000-0002-8950-1850"},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Arjan van der Vaart","raw_affiliation_strings":["Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States"],"raw_orcid":"https://orcid.org/0000-0002-8950-1850","affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States","institution_ids":["https://openalex.org/I2613432"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012698288"],"corresponding_institution_ids":["https://openalex.org/I2613432"],"apc_list":null,"apc_paid":null,"fwci":0.1709,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.6537452,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"57","issue":"1","first_page":"85","last_page":"92"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9998999834060669,"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":0.9998999834060669,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9905999898910522,"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":0.9894000291824341,"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/uracil","display_name":"Uracil","score":0.791154682636261},{"id":"https://openalex.org/keywords/thymine","display_name":"Thymine","score":0.790107250213623},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.6561185717582703},{"id":"https://openalex.org/keywords/umbrella-sampling","display_name":"Umbrella sampling","score":0.5741639137268066},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5625851154327393},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.5082854628562927},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4865371286869049},{"id":"https://openalex.org/keywords/guanine","display_name":"Guanine","score":0.484321266412735},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.442574143409729},{"id":"https://openalex.org/keywords/energy-landscape","display_name":"Energy landscape","score":0.41412580013275146},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.4113401770591736},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3683020770549774},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3481610417366028},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3138607442378998},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.31308168172836304},{"id":"https://openalex.org/keywords/nucleotide","display_name":"Nucleotide","score":0.2134559452533722},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07543155550956726}],"concepts":[{"id":"https://openalex.org/C2779554091","wikidata":"https://www.wikidata.org/wiki/Q182990","display_name":"Uracil","level":3,"score":0.791154682636261},{"id":"https://openalex.org/C2776858809","wikidata":"https://www.wikidata.org/wiki/Q171973","display_name":"Thymine","level":3,"score":0.790107250213623},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.6561185717582703},{"id":"https://openalex.org/C128747166","wikidata":"https://www.wikidata.org/wiki/Q7881414","display_name":"Umbrella sampling","level":3,"score":0.5741639137268066},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5625851154327393},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.5082854628562927},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4865371286869049},{"id":"https://openalex.org/C2778301229","wikidata":"https://www.wikidata.org/wiki/Q169313","display_name":"Guanine","level":4,"score":0.484321266412735},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.442574143409729},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.41412580013275146},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.4113401770591736},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3683020770549774},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3481610417366028},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3138607442378998},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.31308168172836304},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.2134559452533722},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07543155550956726},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014498","descriptor_name":"Uracil","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014498","descriptor_name":"Uracil","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014498","descriptor_name":"Uracil","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.6b00660","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00660","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:27976883","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27976883","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":[{"score":0.8899999856948853,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1563139097","https://openalex.org/W1597842671","https://openalex.org/W1968754848","https://openalex.org/W1976499671","https://openalex.org/W1983951091","https://openalex.org/W1990356245","https://openalex.org/W1991047673","https://openalex.org/W1993177346","https://openalex.org/W1996075279","https://openalex.org/W2013803515","https://openalex.org/W2015261322","https://openalex.org/W2016040122","https://openalex.org/W2024762727","https://openalex.org/W2033102150","https://openalex.org/W2041804048","https://openalex.org/W2043995349","https://openalex.org/W2051039246","https://openalex.org/W2052650104","https://openalex.org/W2058244371","https://openalex.org/W2067174909","https://openalex.org/W2074718022","https://openalex.org/W2083405943","https://openalex.org/W2086634221","https://openalex.org/W2093463166","https://openalex.org/W2100380699","https://openalex.org/W2106140689","https://openalex.org/W2112154906","https://openalex.org/W2115328412","https://openalex.org/W2131711535","https://openalex.org/W2132262459","https://openalex.org/W2139064328","https://openalex.org/W2148493354","https://openalex.org/W2148674110","https://openalex.org/W2156016724","https://openalex.org/W2241751620","https://openalex.org/W2313141362","https://openalex.org/W2325449676","https://openalex.org/W2502701244","https://openalex.org/W2962895620","https://openalex.org/W3105581675","https://openalex.org/W4211068716"],"related_works":["https://openalex.org/W1522051322","https://openalex.org/W2065438617","https://openalex.org/W2006094627","https://openalex.org/W2008794028","https://openalex.org/W2168580805","https://openalex.org/W2085887851","https://openalex.org/W1990025216","https://openalex.org/W2047972624","https://openalex.org/W2087390147","https://openalex.org/W2329079694"],"abstract_inverted_index":{"An":[0],"accurate":[1],"and":[2,39,62,65,76,88,109],"efficient":[3],"implementation":[4],"of":[5,35,47,56,79,112],"the":[6,36,48,100,113],"six":[7],"DNA":[8],"base":[9,37,116],"pair":[10],"parameters":[11,14],"as":[12],"order":[13],"for":[15],"enhanced":[16],"sampling":[17,54],"simulations":[18,55],"is":[19,50,95],"presented.":[20],"The":[21,91],"parameter":[22],"definitions":[23],"are":[24,71],"defined":[25],"by":[26,52],"vector":[27],"algebra":[28],"operations":[29],"on":[30],"a":[31,77],"reduced":[32],"atomic":[33],"set":[34],"pair,":[38],"correlate":[40],"very":[41],"well":[42],"with":[43,106],"standard":[44],"definitions.":[45],"Application":[46],"model":[49],"illustrated":[51],"umbrella":[53],"propeller":[57,74],"twisting":[58,75],"within":[59,108],"AT/AT,":[60],"AA/TT,":[61],"AC/GT":[63],"steps":[64],"their":[66],"uracil":[67],"analogs.":[68],"Strong":[69],"correlations":[70],"found":[72],"between":[73],"number":[78],"conformational":[80,102],"parameters,":[81],"including":[82],"buckle,":[83],"opening,":[84],"BI/BII":[85],"backbone":[86],"configuration,":[87],"sugar":[89],"puckering.":[90],"thymine":[92,114],"methyl":[93],"group":[94],"observed":[96],"to":[97],"notably":[98],"alter":[99],"local":[101],"free":[103],"energy":[104],"landscape,":[105],"effects":[107],"directly":[110],"upstream":[111],"containing":[115],"pair.":[117]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}