Development of KiBank, a database supporting structure-based drug design
Development of KiBank, a database supporting structure-based drug design
复制标题
DOI：
10.1016/j.compbiolchem.2004.09.003
复制
发表时间：
2004-12-01
影响因子：
3.1
通讯作者：
Nakata, K
中科院分区：
文献类型：
--
作者：
Zhang, JW;Aizawa, M;Nakata, K
KiBank是一个包含目标蛋白质和化学物质的3D结构的抑制常数（Ki）值数据库。K-i值是从通过PubMed检索的同行评审文献中累积的。目标蛋白质的三维结构文件来源于蛋白质数据库（PDB），而化合物的二维结构文件则与Ki值一起收集，然后转换为三维结构文件。在KiBank中，通过能量最小化优化含氢原子的化学和蛋白质3D结构，并分别以MDL MOL和PDB格式存储。KiBank旨在支持基于结构的药物设计。它提供了蛋白质和化学品的结构文件，可用于通过自动对接方法进行虚拟筛选，而K-i值可用于对接/评分组合的测试，程序参数设置和经验评分函数的校准。此外，KiBank中的化学结构和相应的K-i值对于基于定量构效关系（QSAR）技术的先导化合物优化非常有用。KiBank每天更新，可在http://kibank.iis.u-tokyo.ac.jp/上免费获得。截至2004年8月，KiBank包含8000个K-i值，超过6000种化学物质和166种蛋白质，涵盖受体和酶的亚型。(C)2004爱思唯尔有限公司保留所有权利。
KiBank is a database of inhibition constant (K-i) values with 3D structures of target proteins and chemicals. K-i 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 K-i 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 K-i 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 K-i 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 K-i values, over 6000 chemicals and 166 proteins covering the subtypes of receptors and enzymes. (C) 2004 Elsevier Ltd. All rights reserved.