PDBbind database
Introduction
The PDBbind database is developed through collaborations between Prof. Shaomeng Wang's group at the University of Michigan in USA and Prof. Renxiao Wang's group at the Shanghai Institute of Organic Chemistry in China. The PDBbind database is created to provide 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). 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. The PDBbind database was first released to the public in May, 2004.
This web site, i.e. PDBbind-CN, hosts a mirror site of the PDBbind database, which is maintained by Prof. Renxiao Wang's group at the Shanghai Institute of Organic Chemistry. This web site is created to better serve the local users in China and surrounding countries. The web interface of PDBbind-CN might be different from PDBbind but the contents of PDBbind and PDBbind-CN are identical. All registered users of PDBbind will be granted access to PDBbind-CN as well.
Current release
The PDBbind database is currently updated on an annual base. The current release is version 2007. It takes account for the protein-ligand complexes officially released by PDB before Jan 1st, 2007. In brief, this release provides binding data of 3,214 protein-ligand complexes. All of these binding affinity data are cited from original references. For each entry in this set, a table summarizing its basic information is available on this web site. Our web site also supports interactive substructure / similarity search among these complexes. A total of 1,300 protein-ligand complexes are further selected into the "refined set" with concerns on the quality of complex structures and binding data. Structures of all complexes in the refined set are available in properly processed formats for download so that they can be readily utilized by molecular modeling programs. A "core set" is also provided as a non-redundant sampling of the "refined set". Currently, this core set includes a total of 70 different proteins and 210 protein-ligand complexes.
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. Please go to the "[register]" page to register.
References
[1] Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. "The PDBbind Database: Methodologies and updates", J. Med. Chem., 2005; 48(12); 4111-4119.
[2] Wang, R.; Fang, X.; Lu, Y.; Wang, S. "The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures", J. Med. Chem., 2004; 47(12); 2977-2980.