PDBbind

The PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). All of the binding affinity data compiled in the PDBbind database were cited from original references.


http://www.pdbbind.org/





Jchem and Marvin implementation

Ferenc wrote:

The PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). All of the binding affinity data compiled in the PDBbind database were cited from original references. http://www.pdbbind.org/ Jchem and Marvin implementation

http://www.pdbbind.org.cn/


http://sw16.im.med.umich.edu/databases/pdbbind/index.jsp








Introduction. 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 an essential linkage between energetic and structural information of these complexes, which may be helpful for various studies on molecular recognition occurred in biological systems.





The PDBbind database was first released to the public in May, 2004. The PDBbind database is now developed through collaboration between Prof. Renxiao Wang's group at the Shanghai Institute of Organic Chemistry in China and Prof. Shaomeng Wang's group at the University of Michigan in USA. This web site, i.e. PDBbind-CN, is developed by Prof. Renxiao Wang's group at the Shanghai Institute of Organic Chemistry as a mirror site of the original PDBbind site (http://www.pdbbind.org/). It 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.








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Current release. The PDBbind database is now updated on an annual base. The current release is version 2008, which is based on the contents of PDB officially released on Jan 1st, 2008. As a new feature of this version, all four major categories of complexes in PDB, including protein-ligand, nucleic acid-ligand, protein-nucleic acid, and protein-protein complexes, are considered. Binding affinity data of a total of 4,300 complexes are given in this version, which were collected out of >11,300 references. Moreover, the “refined set” and the “core set” are provided as high-quality data sets of protein-ligand complexes especially for docking/scoring studies. Click here for a brief introduction to the PDBbind database.








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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.








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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.