groovDB in 2026: a community-editable database of small molecule biosensors

Nucleic Acids Res. 2025 Oct 31:gkaf1074. doi: 10.1093/nar/gkaf1074. Online ahead of print.

ABSTRACT

The groovDB database (https://groov.bio) was launched in 2022 with the goal of organizing information on prokaryotic ligand-inducible transcription factors (TFs). This class of proteins is important in fundamental areas of microbiology research and for biotechnological applications that develop biosensors for diagnostics, enzyme screening, and real-time metabolite tracking. Uniquely, groovDB contains stringently curated, literature-referenced data on both TF:DNA and TF:ligand interactions. Here, we describe a major technical update to groovDB, making the database community-editable and adding several advanced features. Users can now add new TF entries and update existing entries using a simple online form. New user interface elements display interactive protein structures and DNA-binding motifs. Updated query methods enable database searches via text, chemical similarity, and attribute filtering. A new data architecture reduces page load time by five-fold. Finally, the number of TF entries has more than doubled and all source code is now open-access.

PMID:41171132 | DOI:10.1093/nar/gkaf1074