Welcome to the PDBbind Database!

The PDBbind database is developed in Dr. Shaomeng Wang's group at the University of Michigan. 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 this database are cited from original references. Click here for a brief introduction to the PDBbind database.
Current release. The current release is version 2007, which means that it takes account for the protein-ligand complexes officially released by PDB before Jan 1st, 2007. In summary, this release provides binding data of 3,214 protein-ligand complexes. For each entry in this set, a table summarizing its basic information is available our web site. A total of 1,300 protein-ligand complexes are selected to form the "refined set" with concerns on the quality of structures and binding data, which is compiled particularly for docking/scoring studies. For each entry in this set, properly processed structure files are provided so that they can be readily utilized by molecular modeling programs. Our web site also supports interactive substructure / similarity search within this data set. Another "core set" provides a non-redundant sampling of the "refined set". Currently, a total of 70 different proteins and 210 entries are included in this set.
Availability. Academic/governmental users may access the PDBbind database for free under a license agreement. Industrial/commercial users may access this database with a moderate amount of subscription fee. Please follow the instructions on the "enroll" page.
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.
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  • This web site is maintained by Dr. Xueliang Fang and Dr. Renxiao Wang. Latest update: June, 2007.
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