Source 1primary paper2026MED
Toolkit/groovDB
groovDB
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
The groovDB database (https://groov.bio) was launched in 2022 with the goal of organizing information on prokaryotic ligand-inducible transcription factors (TFs). Uniquely, groovDB contains stringently curated, literature-referenced data on both TF:DNA and TF:ligand interactions.
Usefulness & Problems
Why this is useful
groovDB is a database for prokaryotic ligand-inducible transcription factors with curated TF:DNA and TF:ligand interaction data. The 2026 update adds community editing, interactive structure and motif displays, and expanded search features.; organizing information on prokaryotic ligand-inducible transcription factors; searching TF entries by text, chemical similarity, and attribute filtering; supporting biosensor development use cases including diagnostics, enzyme screening, and real-time metabolite tracking
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groovDB is a database for prokaryotic ligand-inducible transcription factors with curated TF:DNA and TF:ligand interaction data. The 2026 update adds community editing, interactive structure and motif displays, and expanded search features.
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organizing information on prokaryotic ligand-inducible transcription factors
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searching TF entries by text, chemical similarity, and attribute filtering
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supporting biosensor development use cases including diagnostics, enzyme screening, and real-time metabolite tracking
Problem solved
It centralizes literature-referenced biosensor-relevant transcription factor data that would otherwise be scattered across publications. It also improves discoverability through text, chemical similarity, and attribute filtering.; provides a curated, literature-referenced resource linking TF:DNA and TF:ligand interactions; enables community editing and updating of TF entries
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It centralizes literature-referenced biosensor-relevant transcription factor data that would otherwise be scattered across publications. It also improves discoverability through text, chemical similarity, and attribute filtering.
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provides a curated, literature-referenced resource linking TF:DNA and TF:ligand interactions
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enables community editing and updating of TF entries
Problem links
enables community editing and updating of TF entries
LiteratureIt centralizes literature-referenced biosensor-relevant transcription factor data that would otherwise be scattered across publications. It also improves discoverability through text, chemical similarity, and attribute filtering.
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It centralizes literature-referenced biosensor-relevant transcription factor data that would otherwise be scattered across publications. It also improves discoverability through text, chemical similarity, and attribute filtering.
provides a curated, literature-referenced resource linking TF:DNA and TF:ligand interactions
LiteratureIt centralizes literature-referenced biosensor-relevant transcription factor data that would otherwise be scattered across publications. It also improves discoverability through text, chemical similarity, and attribute filtering.
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It centralizes literature-referenced biosensor-relevant transcription factor data that would otherwise be scattered across publications. It also improves discoverability through text, chemical similarity, and attribute filtering.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete measurement method used to characterize an engineered system.
Mechanisms
No mechanism tags yet.
Techniques
Functional AssayTarget processes
transcriptionInput: Chemical
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: sensor
Users access the database through groov.bio and can add or update TF entries using an online form. The abstract also indicates that the source code is open-access.; focused on prokaryotic ligand-inducible transcription factors
Independent follow-up evidence is still limited. Validation breadth across biological contexts is still narrow. Independent reuse still looks limited, so the evidence base may be fragile. No canonical validation observations are stored yet, so context-specific performance remains under-specified.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
All groovDB source code is open-access.
Finally, the number of TF entries has more than doubled and all source code is now open-access.
groovDB contains stringently curated, literature-referenced data on both TF:DNA and TF:ligand interactions.
Uniquely, groovDB contains stringently curated, literature-referenced data on both TF:DNA and TF:ligand interactions.
groovDB displays interactive protein structures and DNA-binding motifs.
New user interface elements display interactive protein structures and DNA-binding motifs.
groovDB supports database searches via text, chemical similarity, and attribute filtering.
Updated query methods enable database searches via text, chemical similarity, and attribute filtering.
Users can add new TF entries and update existing entries in groovDB using a simple online form.
Users can now add new TF entries and update existing entries using a simple online form.
The number of groovDB TF entries has more than doubled.
Finally, the number of TF entries has more than doubled and all source code is now open-access.
TF entry count increase 2 fold
groovDB organizes information on prokaryotic ligand-inducible transcription factors.
The groovDB database (https://groov.bio) was launched in 2022 with the goal of organizing information on prokaryotic ligand-inducible transcription factors (TFs).
A new groovDB data architecture reduces page load time by five-fold.
A new data architecture reduces page load time by five-fold.
page load time reduction 5 fold
The 2026 paper describes a major technical update to groovDB that makes the database community-editable and adds advanced features.
Here, we describe a major technical update to groovDB, making the database community-editable and adding several advanced features.
Approval Evidence
1 source9 linked approval claimsfirst-pass slug groovdb
The groovDB database (https://groov.bio) was launched in 2022 with the goal of organizing information on prokaryotic ligand-inducible transcription factors (TFs). Uniquely, groovDB contains stringently curated, literature-referenced data on both TF:DNA and TF:ligand interactions.
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accessibilitysupports
All groovDB source code is open-access.
Finally, the number of TF entries has more than doubled and all source code is now open-access.
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database contentsupports
groovDB contains stringently curated, literature-referenced data on both TF:DNA and TF:ligand interactions.
Uniquely, groovDB contains stringently curated, literature-referenced data on both TF:DNA and TF:ligand interactions.
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database featuresupports
groovDB displays interactive protein structures and DNA-binding motifs.
New user interface elements display interactive protein structures and DNA-binding motifs.
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database featuresupports
groovDB supports database searches via text, chemical similarity, and attribute filtering.
Updated query methods enable database searches via text, chemical similarity, and attribute filtering.
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database featuresupports
Users can add new TF entries and update existing entries in groovDB using a simple online form.
Users can now add new TF entries and update existing entries using a simple online form.
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database growthsupports
The number of groovDB TF entries has more than doubled.
Finally, the number of TF entries has more than doubled and all source code is now open-access.
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database scopesupports
groovDB organizes information on prokaryotic ligand-inducible transcription factors.
The groovDB database (https://groov.bio) was launched in 2022 with the goal of organizing information on prokaryotic ligand-inducible transcription factors (TFs).
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performance improvementsupports
A new groovDB data architecture reduces page load time by five-fold.
A new data architecture reduces page load time by five-fold.
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technical updatesupports
The 2026 paper describes a major technical update to groovDB that makes the database community-editable and adds advanced features.
Here, we describe a major technical update to groovDB, making the database community-editable and adding several advanced features.
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Comparisons
Source-stated alternatives
The upstream web research summary identifies adjacent regulatory databases including PRODORIC, RegPrecise, RegulonDB, EcoCyc, and DBTBS as nearby alternatives or complementary resources.
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The upstream web research summary identifies adjacent regulatory databases including PRODORIC, RegPrecise, RegulonDB, EcoCyc, and DBTBS as nearby alternatives or complementary resources.
Source-backed strengths
contains both TF:DNA and TF:ligand interaction data; community-editable via a simple online form; includes interactive protein structures and DNA-binding motifs; supports text, chemical similarity, and attribute-based search; source code is open-access
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contains both TF:DNA and TF:ligand interaction data
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community-editable via a simple online form
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includes interactive protein structures and DNA-binding motifs
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supports text, chemical similarity, and attribute-based search
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source code is open-access
Compared with cell-free systems-based high-throughput screening
groovDB and cell-free systems-based high-throughput screening address a similar problem space because they share transcription.
Shared frame: same top-level item type; shared target processes: transcription; same primary input modality: chemical
Compared with qRT-PCR
groovDB and qRT-PCR address a similar problem space because they share transcription.
Shared frame: same top-level item type; shared target processes: transcription
Relative tradeoffs: appears more independently replicated.
groovDB and time-resolved imaging of nucleoid spatial distribution after drug perturbation address a similar problem space because they share transcription.
Shared frame: same top-level item type; shared target processes: transcription; same primary input modality: chemical
Ranked Citations
- 1.