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 is helpful for various computational and statistical studies on molecular recognition occurred in biological systems.
The PDBbind database was originally developed by Prof. Shaomeng Wang's group (http://sw16.im.med.umich.edu) at the University of Michigan in USA, which was first released to the public in May, 2004. This database is now maintained and further developed by Prof. Renxiao Wang's group (http://www.sioc-ccbg.ac.cn) at the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences under a mutual agreement with the University of Michigan. The PDBbind database is now updated on an annual base to keep up with the growth of the Protein Data Bank.
The current release, i.e. version 2016, is based on the contents of PDB officially released by Jan 1st, 2016. This release provides binding data of a total of 16,179 biomolecular complexes, including protein-ligand (13,308), nucleic acid-ligand (118), protein-nucleic acid (777), and protein-protein complexes (1,976), which is currently the largest collection of this kind. Compared to the last release (v.2015), binding data included in this release have increased by 10.66%. All binding data are curated by ourselves from over 29,000 original references. Moreover, a "refined set" and a "core set" are compiled as high-quality data sets of protein-ligand complexes for developing and validating docking/scoring methods. Click here for a brief introduction to the PDBbind database (PDF brochure).
The basic information of each complex in PDBbind is completely open for access (see the [BROWSE] page). Users are required to register under a license agreement in order to utilize the searching functions provided on this web site or to download the contents of PDBbind in bulk. Registration is free of charge to all academic and industrial users. Please go to the [REGISTER] page and follow the instructions to complete registration.
This project is financially supported by the National Natural Science Foundation of China (grants #81430083, #81172984, #21072213, #21102168, #21402230). We are very grateful to Prof. Zenghui (John) Zhang's group at East China Normal University for their aid to the collection of raw data needed by version 2015,2016.