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The PDBbind Database: Collection of Binding Data for the Biomolecular Complexes in the Protein Data Bank
Chao-Yie Yang, University of Michigan
The PDBbind database is created to provide a comprehensive collection of the binding data for the biomolecular complexes deposited in the Protein Data Bank (PDB). The entire PDB is analyzed by a set of computer programs to identify complexes formed between biomacromolecules and/or small molecules. Binding data of these complexes are then collected manually from literature. Binding data as well as structures of these complexes are integrated into a web-based database. The PDBbind database was released to the public for the first time in May 2004, consisting of binding data of 1359 protein-ligand complexes at that time. It has been updated annually since then to keep up with the rapid growth of the PDB. The latest release of PDBbind is version 2008, providing binding data of over 4,200 complexes in PDB. A major expansion of this release is that other classes of biomolecular complexes presented in the PDB, including protein-protein complexes, protein-nucleic acid complexes, and nucleic acid-ligand complexes, are included as well. Thus, the PDBbind database will provide a complete coverage of all types of complexes in the PDB since this release. In addition to the original server of PDBbind maintained in the University of Michigan (http://www.pdbbind.org/), a mirror site (http://www.pdbbind.org.cn/) has been set up in the Shanghai Institute of Organic Chemistry to better serve the users in China and surrounding countries.
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