{"id":"https://openalex.org/W4387251860","doi":"https://doi.org/10.1021/acs.jcim.3c01257","title":"Computational Probing of the Folding Mechanism of Human Telomeric G-Quadruplex DNA","display_name":"Computational Probing of the Folding Mechanism of Human Telomeric G-Quadruplex DNA","publication_year":2023,"publication_date":"2023-10-02","ids":{"openalex":"https://openalex.org/W4387251860","doi":"https://doi.org/10.1021/acs.jcim.3c01257","pmid":"https://pubmed.ncbi.nlm.nih.gov/37782649"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01257","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01257","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/A5062606919","display_name":"Hyeonjun Kim","orcid":"https://orcid.org/0000-0002-8333-2523"},"institutions":[{"id":"https://openalex.org/I4921948","display_name":"Pusan National University","ror":"https://ror.org/01an57a31","country_code":"KR","type":"education","lineage":["https://openalex.org/I4921948"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hyeonjun Kim","raw_affiliation_strings":["Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea","institution_ids":["https://openalex.org/I4921948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066796010","display_name":"Eunae Kim","orcid":"https://orcid.org/0000-0001-8538-7336"},"institutions":[{"id":"https://openalex.org/I152238500","display_name":"Chosun University","ror":"https://ror.org/01zt9a375","country_code":"KR","type":"education","lineage":["https://openalex.org/I152238500"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Eunae Kim","raw_affiliation_strings":["College of Pharmacy, Chosun University, Gwangju 61452, South Korea"],"affiliations":[{"raw_affiliation_string":"College of Pharmacy, Chosun University, Gwangju 61452, South Korea","institution_ids":["https://openalex.org/I152238500"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036465680","display_name":"Youngshang Pak","orcid":"https://orcid.org/0000-0002-7083-8672"},"institutions":[{"id":"https://openalex.org/I4921948","display_name":"Pusan National University","ror":"https://ror.org/01an57a31","country_code":"KR","type":"education","lineage":["https://openalex.org/I4921948"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Youngshang Pak","raw_affiliation_strings":["Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea","institution_ids":["https://openalex.org/I4921948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5036465680"],"corresponding_institution_ids":["https://openalex.org/I4921948"],"apc_list":null,"apc_paid":null,"fwci":1.5564,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.83218555,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"63","issue":"20","first_page":"6366","last_page":"6375"},"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9993000030517578,"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":0.9961000084877014,"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/antiparallel","display_name":"Antiparallel (mathematics)","score":0.9006522297859192},{"id":"https://openalex.org/keywords/g-quadruplex","display_name":"G-quadruplex","score":0.8064213991165161},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.7010003328323364},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.496601402759552},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4678417444229126},{"id":"https://openalex.org/keywords/telomere","display_name":"Telomere","score":0.4654204547405243},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.4282499849796295},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.40521061420440674},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3235754668712616},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22756338119506836},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.19055581092834473},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1886647343635559}],"concepts":[{"id":"https://openalex.org/C142089489","wikidata":"https://www.wikidata.org/wiki/Q1053976","display_name":"Antiparallel (mathematics)","level":3,"score":0.9006522297859192},{"id":"https://openalex.org/C83762044","wikidata":"https://www.wikidata.org/wiki/Q411641","display_name":"G-quadruplex","level":3,"score":0.8064213991165161},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.7010003328323364},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.496601402759552},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4678417444229126},{"id":"https://openalex.org/C177336024","wikidata":"https://www.wikidata.org/wiki/Q14872779","display_name":"Telomere","level":3,"score":0.4654204547405243},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.4282499849796295},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.40521061420440674},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3235754668712616},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22756338119506836},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.19055581092834473},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1886647343635559},{"id":"https://openalex.org/C115260700","wikidata":"https://www.wikidata.org/wiki/Q11408","display_name":"Magnetic field","level":2,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016615","descriptor_name":"Telomere","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016615","descriptor_name":"Telomere","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016615","descriptor_name":"Telomere","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","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":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c01257","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01257","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:37782649","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37782649","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/G825295611","display_name":null,"funder_award_id":"NRF-2022R1A2C2011752","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"}],"funders":[{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1914649288","https://openalex.org/W1969453135","https://openalex.org/W1972820538","https://openalex.org/W1975566644","https://openalex.org/W1975690779","https://openalex.org/W1976499671","https://openalex.org/W1978685619","https://openalex.org/W1980324877","https://openalex.org/W1981225934","https://openalex.org/W1982651819","https://openalex.org/W2007812774","https://openalex.org/W2012219231","https://openalex.org/W2023645508","https://openalex.org/W2030788491","https://openalex.org/W2048748100","https://openalex.org/W2051422063","https://openalex.org/W2053081979","https://openalex.org/W2078024052","https://openalex.org/W2083059706","https://openalex.org/W2089619525","https://openalex.org/W2091138118","https://openalex.org/W2121069954","https://openalex.org/W2122774834","https://openalex.org/W2123891429","https://openalex.org/W2132629607","https://openalex.org/W2143592395","https://openalex.org/W2146411229","https://openalex.org/W2153207180","https://openalex.org/W2172060739","https://openalex.org/W2176289331","https://openalex.org/W2537246643","https://openalex.org/W2545646897","https://openalex.org/W2561564177","https://openalex.org/W2801477501","https://openalex.org/W2895603411","https://openalex.org/W2911794849","https://openalex.org/W2935905363","https://openalex.org/W2937210668","https://openalex.org/W2970740744","https://openalex.org/W2998086267","https://openalex.org/W3006884793","https://openalex.org/W3010816669","https://openalex.org/W3017349264","https://openalex.org/W3039792842","https://openalex.org/W3049710878","https://openalex.org/W3098505498","https://openalex.org/W3099123759","https://openalex.org/W3204386326","https://openalex.org/W3209850868","https://openalex.org/W4252958962","https://openalex.org/W4281709945","https://openalex.org/W4294295937","https://openalex.org/W4301185303","https://openalex.org/W4361190971"],"related_works":["https://openalex.org/W2391450656","https://openalex.org/W2163661389","https://openalex.org/W1970658394","https://openalex.org/W2294405488","https://openalex.org/W1987200161","https://openalex.org/W1970283190","https://openalex.org/W2126319421","https://openalex.org/W2058236842","https://openalex.org/W2363368525","https://openalex.org/W2008120871"],"abstract_inverted_index":{"The":[0],"human":[1,10],"telomeric":[2],"(htel)":[3],"sequences":[4],"in":[5,112],"the":[6,23,45,57,66,75,122],"terminal":[7],"regions":[8],"of":[9,26,32,44,68,77],"telomeres":[11],"form":[12],"diverse":[13],"G-quadruplex":[14],"(GQ)":[15],"structures.":[16],"Despite":[17],"much":[18],"experimental":[19],"efforts":[20],"to":[21,86,104],"elucidate":[22],"folding":[24,35,42,62,84,124],"pathways":[25,43,85],"htel":[27,33,46],"GQ,":[28],"no":[29],"comprehensive":[30],"model":[31],"GQ":[34,47,61,89,123],"has":[36],"been":[37],"presented.":[38],"Here,":[39],"we":[40],"describe":[41],"determined":[48],"by":[49,65,74],"state-of-the-art":[50],"enhanced":[51],"sampling":[52],"molecular":[53],"dynamics":[54],"simulation":[55],"at":[56],"all-atom":[58],"level.":[59],"Briefly,":[60],"is":[63],"initiated":[64],"formation":[67,76],"a":[69],"single-hairpin":[70],"and":[71,97,99,109,125],"then":[72,80],"followed":[73],"double-hairpins,":[78],"which":[79],"branch":[81],"via":[82],"distinct":[83],"produce":[87],"different":[88,129],"topologies":[90],"(antiparallel":[91],"chair,":[92],"antiparallel":[93,113],"basket,":[94],"hybrids":[95],"1":[96],"2,":[98],"parallel":[100],"propeller).":[101],"In":[102],"addition":[103],"these":[105],"double-hairpin":[106],"states,":[107],"three-triad":[108],"two-tetrad":[110],"structures":[111],"backbone":[114],"alignment":[115],"serve":[116],"as":[117],"key":[118],"intermediates":[119],"that":[120],"connect":[121],"transition":[126],"between":[127],"two":[128],"GQs.":[130]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}