{"title":"NNDB：用于预测核酸二级结构稳定性的近邻参数扩展数据库。","authors":"","doi":"10.1016/j.jmb.2024.168549","DOIUrl":null,"url":null,"abstract":"<div><p>Nearest neighbor thermodynamic parameters are widely used for RNA and DNA secondary structure prediction and to model thermodynamic ensembles of secondary structures. The Nearest Neighbor Database (NNDB) is a freely available web resource (<span><span>https://rna.urmc.rochester.edu/NNDB</span><svg><path></path></svg></span>) that provides the functional forms, parameter values, and example calculations. The NNDB provides the 1999 and 2004 set of RNA folding nearest neighbor parameters. We expanded the database to include a set of DNA parameters and a set of RNA parameters that includes m<sup>6</sup>A in addition to the canonical RNA nucleobases. The site was redesigned using the Quarto open-source publishing system. A downloadable PDF version of the complete resource and downloadable sets of nearest neighbor parameters are available.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 17","pages":"Article 168549"},"PeriodicalIF":4.7000,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S002228362400144X/pdfft?md5=0e570dd624af08cd501a916c5bb24b55&pid=1-s2.0-S002228362400144X-main.pdf","citationCount":"0","resultStr":"{\"title\":\"NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures\",\"authors\":\"\",\"doi\":\"10.1016/j.jmb.2024.168549\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Nearest neighbor thermodynamic parameters are widely used for RNA and DNA secondary structure prediction and to model thermodynamic ensembles of secondary structures. The Nearest Neighbor Database (NNDB) is a freely available web resource (<span><span>https://rna.urmc.rochester.edu/NNDB</span><svg><path></path></svg></span>) that provides the functional forms, parameter values, and example calculations. The NNDB provides the 1999 and 2004 set of RNA folding nearest neighbor parameters. We expanded the database to include a set of DNA parameters and a set of RNA parameters that includes m<sup>6</sup>A in addition to the canonical RNA nucleobases. The site was redesigned using the Quarto open-source publishing system. A downloadable PDF version of the complete resource and downloadable sets of nearest neighbor parameters are available.</p></div>\",\"PeriodicalId\":369,\"journal\":{\"name\":\"Journal of Molecular Biology\",\"volume\":\"436 17\",\"pages\":\"Article 168549\"},\"PeriodicalIF\":4.7000,\"publicationDate\":\"2024-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S002228362400144X/pdfft?md5=0e570dd624af08cd501a916c5bb24b55&pid=1-s2.0-S002228362400144X-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Molecular Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S002228362400144X\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Molecular Biology","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S002228362400144X","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
近邻热力学参数被广泛用于 RNA 和 DNA 二级结构预测以及二级结构热力学集合建模。最近邻数据库（NNDB）是一个可免费获取的网络资源（https://rna.urmc.rochester.edu/NNDB），提供函数形式、参数值和计算示例。NNDB 提供了 1999 年和 2004 年的 RNA 折叠近邻参数集。我们对数据库进行了扩展，增加了一组 DNA 参数和一组 RNA 参数，其中除了典型的 RNA 核碱基外，还包括 m6A。我们使用 Quarto 开源出版系统重新设计了网站。可下载 PDF 版本的完整资源和可下载的近邻参数集。
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures
Nearest neighbor thermodynamic parameters are widely used for RNA and DNA secondary structure prediction and to model thermodynamic ensembles of secondary structures. The Nearest Neighbor Database (NNDB) is a freely available web resource (https://rna.urmc.rochester.edu/NNDB) that provides the functional forms, parameter values, and example calculations. The NNDB provides the 1999 and 2004 set of RNA folding nearest neighbor parameters. We expanded the database to include a set of DNA parameters and a set of RNA parameters that includes m6A in addition to the canonical RNA nucleobases. The site was redesigned using the Quarto open-source publishing system. A downloadable PDF version of the complete resource and downloadable sets of nearest neighbor parameters are available.
期刊介绍：
Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions.
Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.
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