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BindingDB specifications


Unique identifier OMICS_03005
Name BindingDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes


  • person_outline Michael K. Gilson

Additional information

Publications for BindingDB

BindingDB citations


TBC2target: A Resource of Predicted Target Genes of Tea Bioactive Compounds

Front Plant Sci
PMCID: 5827417
PMID: 29520288
DOI: 10.3389/fpls.2018.00211
call_split See protocol

[…] small molecule as query in its background database, which is a large-scale pharmacophore repertoire curated from target information in TargetBank (in-house data in PharmMapper project), DrugBank (), BindingDB (), and PDTD (). The server PharmMapper can help to find the optimal mapping poses of the user-uploaded small molecules against all the target genes in PharmTargetDB and the top N potential […]


A computationally driven analysis of the polyphenol protein interactome

Sci Rep
PMCID: 5797150
PMID: 29396566
DOI: 10.1038/s41598-018-20625-5
call_split See protocol

[…] was searched in CHEBI database, containing ~100,000 entries, for corresponding CHEBI ID’s based on standardised SMILES. Polyphenol-protein interactions were mined from the STITCH, Pathway Commons and BindingDB databases, which collect information from multiple and often redundant databases, using name and CHEBI ID. Depending on the database, the term ‘interaction’ can either refer to direct bindin […]


Docking based inverse virtual screening: methods, applications, and challenges

Biophysics Rep
PMCID: 5860130
PMID: 29577065
DOI: 10.1007/s41048-017-0045-8

[…] derived from a protein–ligand complex structure database like sc-PDB, or constructed by collecting information from publically accessible drug–target databases such as SuperTarget (Günther et al. ), BindingDB (Liu et al. ), and DrugBank (Wishart et al. ), as listed in Table . It should be noted that information in the later databases is redundant. The 3D structures of proteins need to be download […]


Prediction of GPCR Ligand Binding Using Machine Learning Algorithms

PMCID: 5831789
PMID: 29666662
DOI: 10.1155/2018/6565241

[…] provided in the GLASS database and predicted ligands that may bind to them (provided in the Supplementary Materials ()). To measure the prediction accuracy, we downloaded protein-ligand bindings from BindingDB []. We selected 9 GPCRs which are common in BindingDB, Cyscore, and the proposed bindings and counted the number of predictions found in the BindingDB. To count true negatives (which is not […]


Quantitative Structure Activity Relationship Model for HCVNS5B inhibitors based on an Antlion Optimizer Adaptive Neuro Fuzzy Inference System

Sci Rep
PMCID: 5784174
PMID: 29367667
DOI: 10.1038/s41598-017-19122-y

[…] build the QSAR model, which comprised 579 HCV NS5B inhibitors, (PIC50 < ~14) and 450 non-HCVNS5B inhibitors (PIC50 > ~14). These compounds were collected from previous studies and extracted from the BindingDB and CHEMBL databases,. The chemical descriptors were calculated using the DataWarrior package. Thus, DataWarrior was used to calculate the properties of compound such as the drug-likeness, a […]


A census of P. longum’s phytochemicals and their network pharmacological evaluation for identifying novel drug like molecules against various diseases, with a special focus on neurological disorders

PLoS One
PMCID: 5761900
PMID: 29320554
DOI: 10.1371/journal.pone.0191006

[…] ]. Compiled dataset was filtered to remove duplicate entries. Human proteins targeted by the phytochemicals were predicted from STITCH 5.0 (Search Tool for Interactions of Chemicals and proteins) [], BindingDB [], SwissTargetPrediction [] and PCIDB.The protein-chemical interaction reported in STITCH comes from the manually curated datasets including DrugBank [] GLIDA [], Matador [], TTD (Therapeut […]


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BindingDB institution(s)
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
BindingDB funding source(s)
Supported by National Institutes of Health (NIH) [R01GM070064].

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