Department of Computer Science, University of California, Irvine, Irvine, California 92697, United States.
Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States.
J Chem Inf Model. 2023 Feb 27;63(4):1114-1123. doi: 10.1021/acs.jcim.2c01359. Epub 2023 Feb 17.
We introduce RMechDB, an open-access platform for aggregating, curating, and distributing reliable data about elementary radical reaction steps for computational radical reaction modeling and prediction. RMechDB contains over 5,300 elementary radical reaction steps, each with a single transition state at or around room temperature. These elementary step reactions are manually curated plausible arrow-pushing steps for organic radical reactions. The steps were taken from a variety of sources. Over 2,000 mechanistic steps were extracted from textbooks and/or constructed from research publications. Another 3,000 were taken from gas-phase atmospheric reactions of isoprene and other organic molecules on the MCM (Master Chemical Mechanism) Web site. Reactions are encoded in the SMIRKS format with accurate atom mapping and annotations for arrow-pushing mechanisms. At its core, RMechDB consists of a database schema with an online interactive search interface and a request portal for downloading the raw form of elementary step reactions with their metadata. It also offers an interface for submitting new reactions to RMechDB and expanding the data set through community contributions. Although there are several applications for RMechDB, it is primarily designed as a central platform of radical elementary steps with a unified and structured representation. We believe that this open access to this data and platform enables the extension of data-driven models for chemical reaction predictions and other chemoinformatics predictive tasks.
我们介绍了 RMechDB，这是一个开放获取的平台，用于聚合、整理和分发关于基本自由基反应步骤的可靠数据，以进行计算自由基反应建模和预测。RMechDB 包含超过 5300 个基本自由基反应步骤，每个步骤在室温或接近室温时只有一个过渡态。这些基本步骤反应是经过人工整理的有机自由基反应的合理箭头推动步骤。这些步骤来自各种来源。超过 2000 个机理步骤是从教科书和/或研究出版物中提取的。另外 3000 个来自 MCM（主化学机制）网站上异戊二烯和其他有机分子的气相大气反应。反应以 SMIRKS 格式编码，并具有准确的原子映射和用于箭头推动机制的注释。RMechDB 的核心是一个数据库模式，具有在线交互式搜索界面和请求门户，用于下载具有元数据的基本步骤反应的原始形式。它还提供了一个提交新反应到 RMechDB 的接口，并通过社区贡献扩展数据集。尽管 RMechDB 有几个应用，但它主要是作为一个具有统一和结构化表示的自由基基本步骤的中央平台设计的。我们相信，这种对数据和平台的开放访问，使基于数据的化学反应预测模型和其他化学信息学预测任务得到扩展。
