NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures

IF 4.7 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Biology Pub Date : 2024-09-01 DOI:10.1016/j.jmb.2024.168549

引用次数: 0

Abstract

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.

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NNDB：用于预测核酸二级结构稳定性的近邻参数扩展数据库。

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。

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来源期刊

Journal of Molecular Biology 生物-生化与分子生物学

CiteScore

11.30

自引率

1.80%

发文量

412

审稿时长

28 days

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