The PDBbind database: Methodologies and updates
The PDBbind database: Methodologies and updates
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DOI：
10.1021/jm048957q
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发表时间：
2005-06-16
影响因子：
7.3
通讯作者：
Wang, SM
中科院分区：
文献类型：
--
作者：
Wang, RX;Fang, XL;Wang, SM
我们开发了PDBbind数据库，以提供蛋白质数据库（PDB）中蛋白质-配体复合物的结合亲和力的全面收集。本文给出了最新版本的完整描述，即，2003年版，这是我们最近报告的工作的更新。在PDB第107号发布（2004年1月）的23790个条目中，有5897个条目被鉴定为符合我们定义的蛋白质-配体复合物。从与这些复合物相关的参考文献中检索了其中1622个的实验测定的结合亲和力（K-d、K-i和IC 50）。共选择900个复合物，形成一个“精炼集”，这是特别有价值的对接和评分研究的标准数据集。所有最终数据，包括结合亲和力数据、参考文献引用和处理的结构文件，都已纳入可在http://www.pdbbind.org/在线访问的PDBbind数据库中。
We have developed the PDBbind database to provide a comprehensive collection of binding affinities for the protein-ligand complexes in the Protein Data Bank (PDB). This paper gives a full description of the latest version, i.e., version 2003, which is an update to our recently reported work. Out of 23 790 entries in the PDB release No.107 (January 2004), 5897 entries were identified as protein-ligand complexes that meet our definition. Experimentally determined binding affinities (K-d, K-i, and IC50) for 1622 of these were retrieved from the references associated with these complexes. A total of 900 complexes were selected to form a "refined set", which is of particular value as a standard data set for docking and scoring studies. All of the final data, including binding affinity data, reference citations, and processed structural files, have been incorporated into the PDBbind database accessible on-line at http://www.pdbbind.org/.