{"created":"2023-05-15T14:59:17.154393+00:00","id":80437,"links":{},"metadata":{"_buckets":{"deposit":"847fec7a-9ba7-4145-a862-8bb620ed1679"},"_deposit":{"created_by":1,"id":"80437","owners":[1],"pid":{"revision_id":0,"type":"depid","value":"80437"},"status":"published"},"_oai":{"id":"oai:repo.qst.go.jp:00080437","sets":["1"]},"author_link":["888256","888254","888255","888252","888258","888259","888251","888253","888257"],"item_8_biblio_info_7":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2020-09","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"9","bibliographicPageEnd":"5935","bibliographicPageStart":"5925","bibliographicVolumeNumber":"16","bibliographic_titles":[{"bibliographic_title":"Journal of the Computational and Theoretical Chemistry"}]}]},"item_8_description_5":{"attribute_name":"抄録","attribute_value_mlt":[{"subitem_description":"Can current simulations quantitatively predict the stability of ribonucleic acids (RNAs)? In this research, we apply a free-energy perturbation simulation of RNAs containing inosine, a modified ribonucleic base, to the derivation of RNA nearest-neighbor parameters. A parameter set derived solely from 30 simulations was used to predict the free-energy difference of the RNA duplex with a mean unbiased error of 0.70 kcal/mol, which is a level of accuracy comparable to that obtained with parameters derived from 25 experiments. We further show that the error can be lowered to 0.60 kcal/mol by combining the simulation-derived free-energy differences with experimentally measured differences. This protocol can be used as a versatile method for deriving nearest-neighbor parameters of RNAs with various modified bases.","subitem_description_type":"Abstract"}]},"item_8_publisher_8":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"American Chemical Society"}]},"item_8_relation_14":{"attribute_name":"DOI","attribute_value_mlt":[{"subitem_relation_type_id":{"subitem_relation_type_id_text":"10.1021/acs.jctc.0c00270","subitem_relation_type_select":"DOI"}}]},"item_8_relation_17":{"attribute_name":"関連サイト","attribute_value_mlt":[{"subitem_relation_type_id":{"subitem_relation_type_id_text":"https://pubs.acs.org/doi/abs/10.1021/acs.jctc.0c00270","subitem_relation_type_select":"URI"}}]},"item_8_source_id_9":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"1549-9618","subitem_source_identifier_type":"ISSN"}]},"item_access_right":{"attribute_name":"アクセス権","attribute_value_mlt":[{"subitem_access_right":"metadata only access","subitem_access_right_uri":"http://purl.org/coar/access_right/c_14cb"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Sakuraba, Shun"}],"nameIdentifiers":[{"nameIdentifier":"888251","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Iwakiri, Junichi"}],"nameIdentifiers":[{"nameIdentifier":"888252","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Hamada, Michiaki"}],"nameIdentifiers":[{"nameIdentifier":"888253","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Kameda, Tomoshi"}],"nameIdentifiers":[{"nameIdentifier":"888254","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Tsuji, Genichiro"}],"nameIdentifiers":[{"nameIdentifier":"888255","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Kimura, Yasuaki"}],"nameIdentifiers":[{"nameIdentifier":"888256","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Abe, Hiroshi"}],"nameIdentifiers":[{"nameIdentifier":"888257","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Asai, Kiyoshi"}],"nameIdentifiers":[{"nameIdentifier":"888258","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Sakuraba, Shun","creatorNameLang":"en"}],"nameIdentifiers":[{"nameIdentifier":"888259","nameIdentifierScheme":"WEKO"}]}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourcetype":"journal article","resourceuri":"http://purl.org/coar/resource_type/c_6501"}]},"item_title":"Free-energy calculation of ribonucleic inosines and its application to nearest-neighbor parameters","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Free-energy calculation of ribonucleic inosines and its application to nearest-neighbor parameters"}]},"item_type_id":"8","owner":"1","path":["1"],"pubdate":{"attribute_name":"公開日","attribute_value":"2020-09-08"},"publish_date":"2020-09-08","publish_status":"0","recid":"80437","relation_version_is_last":true,"title":["Free-energy calculation of ribonucleic inosines and its application to nearest-neighbor parameters"],"weko_creator_id":"1","weko_shared_id":-1},"updated":"2023-05-15T21:32:18.805220+00:00"}