Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Berne, Switzerland.
J Chem Inf Model. 2017 Apr 24;57(4):700-709. doi: 10.1021/acs.jcim.7b00020. Epub 2017 Apr 11.
To better understand chemical space we recently enumerated the database GDB-17 containing 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogen following the simple rules of chemical stability and synthetic feasibility. However, due to the combinatorial explosion caused by systematic enumeration GDB-17 is strongly biased toward the largest, functionally and stereochemically most complex molecules and far too large for most virtual screening tools. Herein we selected a much smaller subset of GDB-17, called the fragment database FDB-17, which contains 10 million fragmentlike molecules evenly covering a broad value range for molecular size, polarity, and stereochemical complexity. The database is available at www.gdb.unibe.ch for download and free use, together with an interactive visualization application and a Web-based nearest neighbor search tool to facilitate the selection of new fragment-sized molecules for chemical synthesis.
为了更好地理解化学空间，我们最近对包含 1664 亿种可能的分子的数据库 GDB-17 进行了枚举，这些分子的碳原子、氮原子、氧原子、硫原子和卤原子数量不超过 17 个，并且遵循化学稳定性和合成可行性的简单规则。然而，由于系统枚举造成的组合爆炸，GDB-17 强烈偏向于最大、功能和立体化学最复杂的分子，而且对于大多数虚拟筛选工具来说太大了。在此，我们选择了 GDB-17 的一个小得多的子集，称为片段数据库 FDB-17，其中包含 1000 万个片段样分子，均匀覆盖了分子大小、极性和立体化学复杂性的广泛值范围。该数据库可在 www.gdb.unibe.ch 上下载和免费使用，同时提供一个交互式可视化应用程序和一个基于网络的最近邻搜索工具，以方便选择用于化学合成的新片段大小的分子。
