{"id":"https://openalex.org/W7162877978","doi":"https://doi.org/10.1093/bib/bbag252","title":"Untangling or further entangling? Theoretical expansion of the structural landscape of nucleic acid quadruplexes and modeling with 3D-NuS-Qplex","display_name":"Untangling or further entangling? Theoretical expansion of the structural landscape of nucleic acid quadruplexes and modeling with 3D-NuS-Qplex","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7162877978","doi":"https://doi.org/10.1093/bib/bbag252","pmid":"https://pubmed.ncbi.nlm.nih.gov/42217192"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag252","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag252","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag252","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000179508","display_name":"Thenmalarchelvi Rathinavelan","orcid":"https://orcid.org/0000-0002-1142-0583"},"institutions":[{"id":"https://openalex.org/I65181880","display_name":"Indian Institute of Technology Hyderabad","ror":"https://ror.org/01j4v3x97","country_code":"IN","type":"education","lineage":["https://openalex.org/I65181880"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Thenmalarchelvi Rathinavelan","raw_affiliation_strings":["Department of Biotechnology, Indian Institute of Technology Hyderabad , Kandi, Telangana 502284 ,"],"raw_orcid":"https://orcid.org/0000-0002-1142-0583","affiliations":[{"raw_affiliation_string":"Department of Biotechnology, Indian Institute of Technology Hyderabad , Kandi, Telangana 502284 ,","institution_ids":["https://openalex.org/I65181880"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019687268","display_name":"Sruthi Sundaresan","orcid":"https://orcid.org/0000-0002-3430-6070"},"institutions":[{"id":"https://openalex.org/I65181880","display_name":"Indian Institute of Technology Hyderabad","ror":"https://ror.org/01j4v3x97","country_code":"IN","type":"education","lineage":["https://openalex.org/I65181880"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sruthi Sundaresan","raw_affiliation_strings":["Department of Biotechnology, Indian Institute of Technology Hyderabad , Kandi, Telangana 502284 ,"],"raw_orcid":"https://orcid.org/0000-0002-3430-6070","affiliations":[{"raw_affiliation_string":"Department of Biotechnology, Indian Institute of Technology Hyderabad , Kandi, Telangana 502284 ,","institution_ids":["https://openalex.org/I65181880"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5000179508"],"corresponding_institution_ids":["https://openalex.org/I65181880"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.48248227,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9919000267982483,"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":0.9919000267982483,"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":0.000699999975040555,"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/T14099","display_name":"Synthesis and Characterization of Heterocyclic Compounds","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/g-quadruplex","display_name":"G-quadruplex","score":0.758400022983551},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.7005000114440918},{"id":"https://openalex.org/keywords/nucleic-acid","display_name":"Nucleic acid","score":0.5820000171661377},{"id":"https://openalex.org/keywords/oligonucleotide","display_name":"Oligonucleotide","score":0.5688999891281128},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5139999985694885},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.43290001153945923},{"id":"https://openalex.org/keywords/pseudoknot","display_name":"Pseudoknot","score":0.4020000100135803}],"concepts":[{"id":"https://openalex.org/C83762044","wikidata":"https://www.wikidata.org/wiki/Q411641","display_name":"G-quadruplex","level":3,"score":0.758400022983551},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.7005000114440918},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.625},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.5820000171661377},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.5688999891281128},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5139999985694885},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4645000100135803},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.43290001153945923},{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.4020000100135803},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.37790000438690186},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.3443000018596649},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33719998598098755},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.29499998688697815},{"id":"https://openalex.org/C2780428219","wikidata":"https://www.wikidata.org/wiki/Q16952335","display_name":"Cover (algebra)","level":2,"score":0.27950000762939453},{"id":"https://openalex.org/C148625055","wikidata":"https://www.wikidata.org/wiki/Q418840","display_name":"Riboswitch","level":5,"score":0.2732999920845032},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2685000002384186},{"id":"https://openalex.org/C53942344","wikidata":"https://www.wikidata.org/wiki/Q951651","display_name":"Fold (higher-order function)","level":2,"score":0.2671999931335449},{"id":"https://openalex.org/C2988890453","wikidata":"https://www.wikidata.org/wiki/Q5508815","display_name":"Functional diversity","level":2,"score":0.26589998602867126},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.262800008058548}],"mesh":[{"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":"D006801","descriptor_name":"Humans","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":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":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":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019281","descriptor_name":"Dimerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019281","descriptor_name":"Dimerization","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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag252","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag252","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42217192","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42217192","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13221979","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13221979/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag252","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag252","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4822076952","display_name":null,"funder_award_id":"CRG/2022/001825","funder_id":"https://openalex.org/F4320306227","funder_display_name":"Arthritis National Research Foundation"}],"funders":[{"id":"https://openalex.org/F4320306227","display_name":"Arthritis National Research Foundation","ror":"https://ror.org/03abbex33"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1914649288","https://openalex.org/W1969039627","https://openalex.org/W1999364887","https://openalex.org/W2000274610","https://openalex.org/W2007373812","https://openalex.org/W2025248257","https://openalex.org/W2042994965","https://openalex.org/W2078024052","https://openalex.org/W2083059706","https://openalex.org/W2123017921","https://openalex.org/W2123408329","https://openalex.org/W2144175278","https://openalex.org/W2171830519","https://openalex.org/W2472497945","https://openalex.org/W2537246643","https://openalex.org/W2538566404","https://openalex.org/W2538739267","https://openalex.org/W2545646897","https://openalex.org/W2561964990","https://openalex.org/W2615709256","https://openalex.org/W2623595002","https://openalex.org/W2635316626","https://openalex.org/W2766679495","https://openalex.org/W2790912768","https://openalex.org/W2802890827","https://openalex.org/W2889015090","https://openalex.org/W2891084898","https://openalex.org/W2913145970","https://openalex.org/W2945411637","https://openalex.org/W2946459547","https://openalex.org/W2952755628","https://openalex.org/W2966334511","https://openalex.org/W2971016121","https://openalex.org/W3017349264","https://openalex.org/W3080638869","https://openalex.org/W3095118588","https://openalex.org/W3143154750","https://openalex.org/W3152765132","https://openalex.org/W3153808956","https://openalex.org/W3164989187","https://openalex.org/W3177664471","https://openalex.org/W3206907992","https://openalex.org/W4206042670","https://openalex.org/W4283069545","https://openalex.org/W4292566953","https://openalex.org/W4318053912","https://openalex.org/W4321004793","https://openalex.org/W4375955713","https://openalex.org/W4380078858","https://openalex.org/W4387251860","https://openalex.org/W4388307927","https://openalex.org/W4389674654","https://openalex.org/W4392956917","https://openalex.org/W4393035413","https://openalex.org/W4402259363","https://openalex.org/W4402758650","https://openalex.org/W4403472456","https://openalex.org/W4414133847","https://openalex.org/W7125411682"],"related_works":[],"abstract_inverted_index":{"Quadruplexes":[0],"are":[1,86,151],"four-stranded":[2],"nucleic":[3],"acid":[4],"secondary":[5],"structures":[6,19],"that":[7,25,37,71,80,121,145,164],"play":[8],"diverse":[9],"biological":[10],"roles.":[11],"A":[12,182],"recent":[13],"meticulous":[14],"analysis":[15],"of":[16,34,58,101,110,129,138,219,242],"known":[17],"quadruplex":[18,48,130,143,148,162,167,180,198,220,243],"formed":[20],"from":[21,53],"synthetic":[22],"oligonucleotides":[23],"shows":[24],"quadruplexes":[26],"can":[27],"adopt":[28],"33":[29],"distinct":[30],"structural":[31,116,229],"motifs":[32,51,144],"(pairs":[33],"stacked":[35],"quartets)":[36,44],"serve":[38],"as":[39],"scaffolds":[40],"for":[41],"simple":[42],"(multi-layered":[43],"and":[45,61,75,77,205,214,237,246],"complex":[46],"(multi-motifs)":[47],"folds.":[49,131],"These":[50,84],"differ":[52],"one":[54],"another":[55],"in":[56,88,106,158,211],"terms":[57],"interstrand":[59,91],"connectivity":[60,64],"orientation.":[62],"Interstrand":[63],"is":[65,125],"primarily":[66],"governed":[67],"by":[68],"diagonal":[69],"loops":[70,79,85],"connect":[72,81],"alternate":[73],"strands":[74],"lateral":[76],"propeller":[78],"adjacent":[82],"strands.":[83],"absent":[87],"tetramers,":[89],"wherein":[90],"orientation":[92],"alone":[93],"dictates":[94],"the":[95,99,111,126,133,147,156,160,166,170,178,194],"motif":[96],"type.":[97],"While":[98],"diversity":[100,218],"potential":[102],"quadruplex-forming":[103],"sequences,":[104],"enriched":[105],"functionally":[107],"important":[108],"regions":[109],"human":[112],"genome,":[113],"implicates":[114],"their":[115,228],"diversity,":[117],"a":[118,136],"key":[119],"question":[120],"still":[122],"remains":[123],"unresolved":[124],"complete":[127],"landscape":[128,150],"For":[132],"first":[134],"time,":[135],"total":[137],"156":[139],"unique":[140],"theoretically":[141,195],"possible":[142,179,196],"cover":[146],"fold":[149],"mathematically":[152],"devised":[153],"here.":[154],"Given":[155],"difficulty":[157],"capturing":[159],"transient":[161],"intermediates":[163],"mediate":[165],"folding":[168],"process,":[169],"folds":[171,199,221],"reported":[172,222],"here":[173,223],"may":[174,238],"shed":[175],"light":[176],"on":[177],"intermediates.":[181],"tool":[183],"named":[184],"3D-NuS-Qplex":[185],"(https://project.iith.ac.in/3d-nus-qplex/)":[186],"has":[187],"also":[188],"been":[189],"developed":[190],"to":[191,202,209],"model":[192],"all":[193],"energy-minimized":[197],"with":[200],"options":[201],"incorporate":[203],"overhangs":[204],"non-G-quartets":[206],"(in":[207],"addition":[208],"G-quartets)":[210],"both":[212],"DNA":[213],"RNA":[215],"contexts.":[216],"The":[217],"provides":[224],"new":[225],"insight":[226],"into":[227],"complexity,":[230],"which":[231],"appears":[232],"greater":[233],"than":[234],"previously":[235],"anticipated,":[236],"thus":[239],"facilitate":[240],"understanding":[241],"folding,":[244],"quadruplex-protein,":[245],"quadruplex-ligand":[247],"interactions.":[248]},"counts_by_year":[],"updated_date":"2026-08-24T07:32:12.397491","created_date":"2026-05-31T00:00:00"}
