PMechDB: A Public Database of Elementary Polar Reaction Steps

Most online chemical reaction databases are not publicly accessible or are fully downloadable. These databases tend to contain reactions in noncanonicalized formats and often lack comprehensive information regarding reaction pathways, intermediates, and byproducts. Within the few publicly available databases, reactions are typically stored in the form of unbalanced, overall transformations with minimal interpretability of the underlying chemistry. These limitations present significant obstacles to data-driven applications including the development of machine learning models. As an effort to overcome these challenges, we introduce PMechDB, a publicly accessible platform designed to curate, aggregate, and share polar chemical reaction data in the form of elementary reaction steps. Our initial version of PMechDB consists of over 100,000 such steps. In the PMechDB, all reactions are stored as canonicalized and balanced elementary steps, featuring accurate atom mapping and arrow-pushing mechanisms. As an online interactive database, PMechDB provides multiple interfaces that enable users to search, download, and upload chemical reactions. We anticipate that the public availability of PMechDB and its standardized data representation will prove beneficial for chemoinformatics research and education and the development of data-driven, interpretable models for predicting reactions and pathways. PMechDB platform is accessible online at https://deeprxn.ics.uci.edu/pmechdb.