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Table 1 Summary of selected features/uses of databases and applications for exploring molecule–target relationships and their overlapping features with the Drug–Target Database

From: Probing the chemical–biological relationship space with the Drug Target Explorer

 

Drug–Target Explorer

Probe Miner

DGIdb v3.0

DT-Web

BindingDB

Probes and Drugs

Polypharmacology Browser

STITCH

ChEMBLSpace

Carlsbad

SuperTarget

Web app?

X

X

X

X

X

X

X

X

 

X

X

Open-source software?

X

 

X

X—underlying R package only

Unknown

 

X

 

X

  

Search by targets to find drugs?

X

X

X

X

X

X

X—only by PDB-listed ligands

X

X

X

X

Search by drugs to find targets?

X

 

X

X

X

X

X

X

 

X

X

Identification of molecules that are associated with multiple query targets?

X

  

Unknown

 

X

     

Drug structure input?

X

  

X

X

X

X

X

   

Drug name/ID input?

X

 

X

X

X

X

X

X

 

X

X

Visualize drug–target networks?

X

  

X, with user provided drug–target networks

Unknown

  

X

 

X

 

Identify chemically similar drugs?

X

  

X, with user provided drug–target networks

X

Scaffold search

X

X

 

X

X

Allows queries using molecules not in database?

X

  

X, with user provided drug–target networks

X

X

X

X

   

Target organism?

Human

Human

Human

Human

Human and others

Human and others

Human and others

Human and others

Unknown

Human and others

Human and others

Target space?

3.6 k

2.2 k

6.1 k

3.8 k

> 7 k

> 6 k

4.6 k

9.6 mil

Unknown

3.7 k

> 6 k

Chemical space?

280 k

400 k

10 k

4.4 k

> 642 k

> 43 k

870 k

500 k

Unknown

> 435 k

> 196 k

Quantitative interactions?

X

X

 

Unknown

X

X

X

X

X

X

X

Qualitative interaction?

X

X

X

X

 

X

 

Unknown

  

X

Explore polypharmacology?

X

X

X

X

X

X

X

X

X

X

X

Polypharmacologic target enrichment?

X

    

X

 

X

  

X

Comparison of query molecule to HTS drug response datasets?

X

          

Target prediction?

   

X

X

 

X

    

Database access?

Open

Open

Open

Open

Open

Open

Open

Full database requires license

Unknown

Open

Unknown

Last known update

2018

2018

2018

2018

2018

2018

2016

2016

2015

2014

2012

  1. Related tools include Probe Miner [16], DGIdb [8], DT-Web [9], BindingDB [10], Probes and Drugs [15], CarlsbadOne [14], Polypharmacology Browser [11], STITCH [12], ChEMBLSpace [17], and SuperTarget [13]