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The PDBbind database specifications


Unique identifier OMICS_03013
Name The PDBbind database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2017
Registration required Yes
Maintained Yes


  • person_outline Renxiao Wang

Publications for The PDBbind database

The PDBbind database citations


Virtual screening approach to identifying influenza virus neuraminidase inhibitors using molecular docking combined with machine learning based scoring function

PMCID: 5669956
PMID: 29137330
DOI: 10.18632/oncotarget.20915
call_split See protocol

[…] he recent version of RF-Score has outperformed 22 state-of-the-art scoring functions on the PDBbind benchmark []. In the present study, we trained a new implementation of RF-Score on a refined set of the PDBbind database 2016 (containing 3766 protein–ligand complexes), based on 36 RF-Score features and 11 Vina features. The NA-specific scoring function (RF-NA-Score) was trained on 67 NA–ligand com […]


Drug repurposing for aging research using model organisms

Aging Cell
PMCID: 5595691
PMID: 28620943
DOI: 10.1111/acel.12626

[…] plexes and previous validation demonstrated the high accuracy of RF‐Score at this task (Ain et al., ). As RF‐Score v2 required input files in PDBbind format, but not all complexes of interest were in the PDBbind database (Wang et al., ), we created and successfully tested a PDBbind format mimicking pipeline (see Data , Supporting information).Binding affinity = logistic(RFScore, 5, 1). […]


PyMine: a PyMOL plugin to integrate and visualize data for drug discovery

BMC Res Notes
PMCID: 4590260
PMID: 26429562
DOI: 10.1186/s13104-015-1483-3

[…] NsSNP Loader ( is a PyMOL plugin that maps the non-synonymous single nucleotide polymorphism (nsSNP) data on the structure of the protein. The PDBbind database collects binding data for macromolecules and their ligands, and provides some basic display of protein–ligand complexes []. Both NsSNP Loader and PDBbind, however, focus on a sing […]


Combining Machine Learning Systems and Multiple Docking Simulation Packages to Improve Docking Prediction Reliability for Network Pharmacology

PLoS One
PMCID: 3877102
PMID: 24391846
DOI: 10.1371/journal.pone.0083922
call_split See protocol

[…] 1. Molecular structure files: Protein-ligand complex files for re-docking experiments were obtained from the PDBbind database. To validate predictive models with less bias, native ligands of the co-crystallized complexes were first extracted and converted into 2D using Open Babel . For the following dock […]


Binding Modes of Peptidomimetics Designed to Inhibit STAT3

PLoS One
PMCID: 3520966
PMID: 23251591
DOI: 10.1371/journal.pone.0051603

[…] res of the peptidomimetics in complex with the SH2 domain of STAT3 or any other protein from the STAT family are unavailable, the validation was done using a dataset of similar complexes derived from the PDBbind database . The details and analysis of the validation study are available in the Supporting Information (Section S2). The analysis (Figures S13, S14, S15, S16, S17, S18, S19, S20, S21, and […]


Specificity quantification of biomolecular recognition and its implication for drug discovery

Sci Rep
PMCID: 3298884
PMID: 22413060
DOI: 10.1038/srep00309

[…] of tests were taken. First, SPA was tested on a benchmark of protein-ligand complexes which is a high-quality set of 195 protein-ligand complexes selected out from the refined set of 2007 version of the PDBbind database. This benchmark was taken as testing set to compare the performance for a large collection of 16 scoring functions implemented in main-stream commercial softwares or available fro […]


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The PDBbind database institution(s)
State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
The PDBbind database funding source(s)
Supported by the Chinese National Natural Science Foundation [Grant 81172984, 21072213 and Grant 21102168], the Chinese Ministry of Science and Technology [863 High-Tech Grant 2012AA020308], the Science and Technology Development Fund of Macao SAR [Grant 055/ 2013/A2] and by a postdoctoral fellowship from MSD China.

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