NNDB：用于预测核酸二级结构稳定性的扩展近邻参数数据库。
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures.
机构信息
Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA.
Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA; Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
出版信息
J Mol Biol. 2024 Sep 1;436(17):168549. doi: 10.1016/j.jmb.2024.168549. Epub 2024 Mar 24.
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 mA 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.
摘要
最近邻热力学参数广泛用于 RNA 和 DNA 二级结构预测，并用于构建二级结构的热力学系综模型。最近邻数据库（NNDB）是一个免费的网络资源（https://rna.urmc.rochester.edu/NNDB），提供了功能形式、参数值和示例计算。NNDB 提供了 1999 年和 2004 年的 RNA 折叠最近邻参数集。我们扩展了数据库，包括一组 DNA 参数和一组 RNA 参数，其中除了规范的 RNA 碱基外，还包括 mA。该网站使用 Quarto 开源发布系统进行了重新设计。完整资源的可下载 PDF 版本和可下载的最近邻参数集均可获得。
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