LigifyDB: An interactive platform for predicted small molecule biosensors

Prokaryotic transcription factors (TFs) are indispensable small molecule biosensors with broad utility in biotechnology, but only a small fraction have been characterized. To address this issue, recent bioinformatic methods have leveraged information from enzyme reaction databases to predict effector molecules for a given TF. Here, we extend this approach by systematically evaluating 10,965 small molecules within the Rhea enzyme reaction database for association to TFs. Ultimately, this yields the LigifyDB database, which contains predicted associations for 3,164 unique TFs to 1,362 unique small molecules. We then create an interactive web application (https://ligify.groov.bio) to access and query the data, which contains detailed information on chemical ligand structures, TF structures, metadata, genome context, and prediction confidence metrics. The open-access database and user interface for predicted TFs reported herein aims to facilitate the systematic characterization and utility of genetic biosensors for chemical-control of biological systems.