Development of KiBank, a database supporting structure-based drug design

KiBank is a database of inhibition constant (Ki) values with 3D structures of target proteins and chemicals. Ki values were accumulated from peer-reviewed literature searched via PubMed. The 3D structure files of target proteins were originally from Protein Data Bank (PDB), while the 2D structure files of the chemicals were collected together with the Ki values and then converted into 3D ones. In KiBank, the chemical and protein 3D structures with hydrogen atoms were optimized by energy minimization and stored in MDL MOL and PDB format, respectively. KiBank is designed to support structure-based drug design. It provides structure files of proteins and chemicals ready for use in virtual screening through automated docking methods, while the Ki values can be applied for tests of docking/scoring combinations, program parameter settings, and calibration of empirical scoring functions. Additionally, the chemical structures and corresponding Ki values in KiBank are useful for lead optimization based on quantitative structure–activity relationship (QSAR) techniques. KiBank is updated on a daily basis and is freely available at http://kibank.iis.u-tokyo.ac.jp/. As of August 2004, KiBank contains 8000 Ki values, over 6000 chemicals and 166 proteins covering the subtypes of receptors and enzymes.