{"id":"https://openalex.org/W7124162434","doi":"https://doi.org/10.1021/acs.jpclett.5c03438","title":"Characterizing RNA Tetramer Conformational Landscape Using Explainable Machine Learning","display_name":"Characterizing RNA Tetramer Conformational Landscape Using Explainable Machine Learning","publication_year":2026,"publication_date":"2026-01-14","ids":{"openalex":"https://openalex.org/W7124162434","doi":"https://doi.org/10.1021/acs.jpclett.5c03438","pmid":"https://pubmed.ncbi.nlm.nih.gov/41532431"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jpclett.5c03438","doi":"https://doi.org/10.1021/acs.jpclett.5c03438","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jpclett.5c03438","pdf_url":null,"source":{"id":"https://openalex.org/S123480357","display_name":"The Journal of Physical Chemistry Letters","issn_l":"1948-7185","issn":["1948-7185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-3","ki-jl-1","medline","norway-1","poland-200","russia-white-list-1","vabb-shw"],"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":"The Journal of Physical Chemistry Letters","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.26434/chemrxiv-2025-xhhvb","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017806480","display_name":"Sompriya Chatterjee","orcid":"https://orcid.org/0009-0004-8018-9057","observed_orcids":["https://orcid.org/0009-0004-8018-9057"]},"institutions":[{"id":"https://openalex.org/I181233156","display_name":"University of Oregon","ror":"https://ror.org/0293rh119","country_code":"US","type":"education","lineage":["https://openalex.org/I181233156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sompriya Chatterjee","raw_affiliation_strings":["Department of Chemistry and Biochemistry","Materials Science Institute","University of Oregon"],"raw_orcid":"https://orcid.org/0009-0004-8018-9057","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry","institution_ids":[]},{"raw_affiliation_string":"Materials Science Institute","institution_ids":[]},{"raw_affiliation_string":"University of Oregon","institution_ids":["https://openalex.org/I181233156"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033374983","display_name":"Dhiman Ray","orcid":"https://orcid.org/0000-0002-7103-0886","observed_orcids":["https://orcid.org/0000-0002-7103-0886"]},"institutions":[{"id":"https://openalex.org/I181233156","display_name":"University of Oregon","ror":"https://ror.org/0293rh119","country_code":"US","type":"education","lineage":["https://openalex.org/I181233156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dhiman Ray","raw_affiliation_strings":["Department of Chemistry and Biochemistry","Materials Science Institute","University of Oregon"],"raw_orcid":"https://orcid.org/0000-0002-7103-0886","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry","institution_ids":[]},{"raw_affiliation_string":"Materials Science Institute","institution_ids":[]},{"raw_affiliation_string":"University of Oregon","institution_ids":["https://openalex.org/I181233156"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5033374983"],"corresponding_institution_ids":["https://openalex.org/I181233156"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":11.6003,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.98593354,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"17","issue":"4","first_page":"966","last_page":"975"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9639000296592712,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9639000296592712,"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":0.028599999845027924,"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":0.0019000000320374966,"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/explainable-ai","display_name":"explainable AI","score":0.7829999923706055},{"id":"https://openalex.org/keywords/enhanced-sampling","display_name":"enhanced sampling","score":0.8240000009536743},{"id":"https://openalex.org/keywords/free-energy-landscape","display_name":"free energy landscape","score":0.7900000214576721},{"id":"https://openalex.org/keywords/metastable-states","display_name":"metastable states","score":0.8479999899864197},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"dihedral angle","score":0.7680000066757202}],"concepts":[{"id":"https://openalex.org/C2778886173","wikidata":"https://www.wikidata.org/wiki/Q53832","display_name":"Tetramer","level":3,"score":0.6470999717712402},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5633000135421753},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5498999953269958},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.5234000086784363},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47380000352859497},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45350000262260437},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.43709999322891235},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4253000020980835},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.40070000290870667},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3856000006198883},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.35510000586509705},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3294000029563904},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.32919999957084656},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32409998774528503},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.3199999928474426},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.31769999861717224},{"id":"https://openalex.org/C34349673","wikidata":"https://www.wikidata.org/wiki/Q899124","display_name":"Random coil","level":3,"score":0.31630000472068787},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.29919999837875366},{"id":"https://openalex.org/C91852762","wikidata":"https://www.wikidata.org/wiki/Q3307742","display_name":"Fitness landscape","level":3,"score":0.2980000078678131},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.2946000099182129},{"id":"https://openalex.org/C89464430","wikidata":"https://www.wikidata.org/wiki/Q849516","display_name":"Metastability","level":2,"score":0.28870001435279846},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.2802000045776367},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.27810001373291016},{"id":"https://openalex.org/C2777339483","wikidata":"https://www.wikidata.org/wiki/Q647203","display_name":"Conformational change","level":2,"score":0.27730000019073486},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2718000113964081},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.27160000801086426},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.2703000009059906},{"id":"https://openalex.org/C128747166","wikidata":"https://www.wikidata.org/wiki/Q7881414","display_name":"Umbrella sampling","level":3,"score":0.26600000262260437}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D013816","descriptor_name":"Thermodynamics","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},{"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},{"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":4,"locations":[{"id":"doi:10.1021/acs.jpclett.5c03438","doi":"https://doi.org/10.1021/acs.jpclett.5c03438","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jpclett.5c03438","pdf_url":null,"source":{"id":"https://openalex.org/S123480357","display_name":"The Journal of Physical Chemistry Letters","issn_l":"1948-7185","issn":["1948-7185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-3","ki-jl-1","medline","norway-1","poland-200","russia-white-list-1","vabb-shw"],"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":"The Journal of Physical Chemistry Letters","raw_type":"journal-article"},{"id":"doi:10.26434/chemrxiv-2025-xhhvb","doi":"https://doi.org/10.26434/chemrxiv-2025-xhhvb","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2025-xhhvb","pdf_url":null,"source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"doi:10.26434/chemrxiv-2025-xhhvb-v2","doi":"https://doi.org/10.26434/chemrxiv-2025-xhhvb-v2","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2025-xhhvb-v2","pdf_url":null,"source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"pmid:41532431","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41532431","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,"listed_in":[],"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":"The journal of physical chemistry letters","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.26434/chemrxiv-2025-xhhvb","doi":"https://doi.org/10.26434/chemrxiv-2025-xhhvb","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2025-xhhvb","pdf_url":null,"source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/7","score":0.6318352222442627,"display_name":"Affordable and clean energy"}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320312726","display_name":"University of Oregon","ror":"https://ror.org/0293rh119"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1808604268","https://openalex.org/W1989383586","https://openalex.org/W2007662810","https://openalex.org/W2029769696","https://openalex.org/W2046208971","https://openalex.org/W2056211671","https://openalex.org/W2081046982","https://openalex.org/W2087903164","https://openalex.org/W2090247295","https://openalex.org/W2093531960","https://openalex.org/W2101136532","https://openalex.org/W2116413427","https://openalex.org/W2122774834","https://openalex.org/W2135046866","https://openalex.org/W2143592395","https://openalex.org/W2151488213","https://openalex.org/W2170595734","https://openalex.org/W2315297180","https://openalex.org/W2327806745","https://openalex.org/W2337762266","https://openalex.org/W2347178136","https://openalex.org/W2419308189","https://openalex.org/W2495548413","https://openalex.org/W2606461366","https://openalex.org/W2751498235","https://openalex.org/W2782369838","https://openalex.org/W2790441008","https://openalex.org/W2790470680","https://openalex.org/W2800772006","https://openalex.org/W2804234729","https://openalex.org/W2890866192","https://openalex.org/W2951187513","https://openalex.org/W2985288662","https://openalex.org/W3010816669","https://openalex.org/W3014936403","https://openalex.org/W3039792842","https://openalex.org/W3084513853","https://openalex.org/W3168632068","https://openalex.org/W3199951662","https://openalex.org/W3209850868","https://openalex.org/W4200419460","https://openalex.org/W4231415818","https://openalex.org/W4291398283","https://openalex.org/W4319316319","https://openalex.org/W4367692573","https://openalex.org/W4385490283","https://openalex.org/W4391645371","https://openalex.org/W4391881754","https://openalex.org/W4396857207","https://openalex.org/W4400024483","https://openalex.org/W4400459136","https://openalex.org/W4401125342","https://openalex.org/W4403180108","https://openalex.org/W4405429717","https://openalex.org/W4406135117","https://openalex.org/W4406420532","https://openalex.org/W4407178705","https://openalex.org/W4407511837","https://openalex.org/W4408967489","https://openalex.org/W4414287048"],"related_works":[],"abstract_inverted_index":{"The":[0],"conformational":[1,32,67],"flexibility":[2],"of":[3,30,60],"RNA":[4,38,61],"molecules":[5],"enables":[6],"them":[7],"to":[8],"play":[9],"vital":[10],"physiological":[11],"roles,":[12],"including":[13],"carrying":[14],"genetic":[15],"information,":[16],"catalyzing":[17],"reactions,":[18],"and":[19,74,118],"forming":[20],"organelles.":[21],"However,":[22],"this":[23],"structural":[24],"diversity":[25],"complicates":[26],"the":[27,55,126],"quantitative":[28],"sampling":[29,50],"their":[31],"landscape,":[33],"even":[34],"for":[35,121,128],"simple":[36],"single-stranded":[37],"tetramers.":[39,62],"We":[40],"show":[41],"that":[42,98],"combining":[43],"explainable":[44],"artificial":[45],"intelligence":[46],"(XAI)":[47],"with":[48,82],"enhanced":[49],"algorithms":[51],"can":[52],"effectively":[53],"explore":[54],"complex":[56],"free":[57],"energy":[58],"landscapes":[59],"Our":[63],"simulations":[64],"capture":[65],"key":[66,112],"states,":[68],"such":[69],"as":[70],"stacked,":[71],"intercalated,":[72],"nucleobase-flipped,":[73],"random":[75],"coil":[76],"structures,":[77,124],"while":[78],"reproducing":[79],"unbiased":[80],"populations":[81],"much":[83],"less":[84],"computational":[85],"effort":[86],"than":[87],"conventional":[88],"molecular":[89],"dynamics.":[90],"This":[91],"data-driven":[92],"approach":[93],"distinguishes":[94],"several":[95],"metastable":[96],"states":[97],"are":[99],"often":[100],"indistinguishable":[101],"in":[102,130],"standard":[103],"analysis.":[104],"Additionally,":[105],"our":[106],"interpretable":[107],"machine":[108],"learning":[109],"framework":[110],"identifies":[111],"torsion":[113],"angles":[114],"driving":[115],"slow":[116],"transitions":[117],"those":[119],"responsible":[120],"unphysical":[122],"intercalated":[123],"paving":[125],"way":[127],"improvements":[129],"nucleic":[131],"acid":[132],"force":[133],"fields.":[134]},"counts_by_year":[{"year":2026,"cited_by_count":6}],"updated_date":"2026-10-08T09:06:37.294493","created_date":"2026-01-15T00:00:00"}
