Welcome to the PDBbind-CN Database!
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 (http://www.sioc-ccbg.ac.cn) at the Shanghai Institute of Organic Chemistry in China and Prof. Shaomeng Wang's group (http://sw16.im.med.umich.edu) at the University of Michigan in USA. This web site, i.e. PDBbind-CN, is developed and maintained solely by Prof. Renxiao Wang's group as an additional site to the original PDBbind site at http://www.pdbbind.org/. All registered users of PDBbind have been granted access to PDBbind-CN as well.
Current release. The PDBbind database is updated on an annual base 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 officially released on Jan 1st, 2009. This version provides 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 ourselves. 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. Click here for a brief introduction to the PDBbind database (PDF brochure).
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. Technical support contact with: liuhai@mail.sioc.ac.cn
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.
Supporting software. Viewing of 3D molecular structures is powered by ChemAxon. Substructure search is powered by Open Babel. Java2 runtime environment from the Sun Microsystem is also required. Microsoft's Internet Explorer (6.0 or higher) is recommended for browsing this web site.