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Recent advances in experimental and computational techniques for probing or predicting RNA solvent accessibility make this 1D representation of tertiary structures an increasingly attractive feature to explore. Here, we provide a survey of these recent developments, which indicate the emergence of solvent accessibility as a simple 1D property, adding to secondary and tertiary structures for investigating complex structure\u2013function relations of RNAs.<\/jats:p>","DOI":"10.1093\/bib\/bbac112","type":"journal-article","created":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T12:08:57Z","timestamp":1646654937000},"source":"Crossref","is-referenced-by-count":28,"title":["Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4316-5211","authenticated-orcid":false,"given":"Md","family":"Solayman","sequence":"first","affiliation":[{"name":"Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, 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information","author":"Novoa","journal-title":"bioRxiv"},{"key":"2022051813454919800_ref92","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btab391","article-title":"RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis","volume":"37","author":"Zhang","year":"2021","journal-title":"Bioinformatics"},{"key":"2022051813454919800_ref93","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.ymeth.2010.06.007","article-title":"SHAPE-directed RNA secondary structure prediction","volume":"52","author":"Low","year":"2010","journal-title":"Methods"},{"key":"2022051813454919800_ref94","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2020.574485","article-title":"Advances in RNA 3D structure modeling using experimental data","volume":"11","author":"Li","year":"2020","journal-title":"Front 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