groovDB in 2025: A community-editable database of small molecule biosensors

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. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/670880v3_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@17842beorg.highwire.dtl.DTLVardef@65d608org.highwire.dtl.DTLVardef@1c6e2eborg.highwire.dtl.DTLVardef@5bd824_HPS_FORMAT_FIGEXP M_FIG C_FIG