PDBbind database

The PDBbind database is a comprehensive collection of experimentally measured binding affinity data (Kd, Ki, and IC50) for the protein-ligand complexes deposited in the Protein Data Bank (PDB). ^[1][2] It thus provides a link between energetic and structural information of protein-ligand complexes, which is of great value to various studies on molecular recognition occurred in biological systems.

History

The aim of the PDBbind database is to provide a comprehensive collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB). It thus provides a linkage between energetic and structural information of these complexes, which may be used for various studies on molecular recognition occurred in biological systems.

The PDBbind database was first released to the public in May, 2004. The database is now publicly accessible both at the PDBbind-CN site at http://www.pdbbind.org.cn/, which is maintained by Prof. Renxiao Wang's group at the Shanghai Institute of Organic Chemistry in China, as well as the original PDBbind site at http://www.pdbbind.org/, which is maintained by Prof. Shaomeng Wang's group at the University of Michigan in USA.

Current release

The PDBbind database is updated on an annual basis to keep up with the growth of the Protein Data Bank. The current release, i.e. version 2009, is based on the contents of Protein Data Bank released on Jan 1st, 2009.

This release provides two basic types of information:

1. Basic information of >10600 complex structures formed between proteins and small-molecule ligand. The user can display and examine these complex structures on-line. The user can also search through the chemical structures of the ligand molecules included in these complexes.
2. Binding affinity data and structural information for a total of 5,678 biomolecular complexes, including protein-ligand (4277), nucleic acid-ligand (44), protein-nucleic acid (304), and protein-protein complexes (1053), which is the largest collection of this kind so far. Binding data included in version 2009 have increased by 30% as compared to version 2008. All of these data are collected from >14,000 original references by the PDBbind team. They all have been double-checked to ensure that they match the complex structures in the Protein Data Bank. Moreover, a "refined set" and a "core set" are compiled as high-quality data sets of protein-ligand complexes for docking/scoring studies.

Accessibility

The basic information of each complex in PDBbind is totally open for browsing. Users are however required to register for access under a license agreement in order to utilize the full functions provided on this web site or to download the contents of PDBbind. The registration is free of charge to all academic and industrial users.

References

1. ^ Wang R, Fang X, Lu Y, Yang CY, Wang S (June 2005). "The PDBbind database: methodologies and updates". J. Med. Chem. 48 (12): 4111–9. doi:10.1021/jm048957q. PMID 15943484. 
2. ^ Wang R, Fang X, Lu Y, Wang S (June 2004). "The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures". J. Med. Chem. 47 (12): 2977–80. doi:10.1021/jm030580l. PMID 15163179. 

External links

The Latest domain name of PDBbind-CN server is: http://www.pdbbind-cn.org/ http://www.pdbbind-cn.net/