Cao Yiqun, Charisi Anna, Cheng Li-Chang, Jiang Tao, Girke Thomas
Department of Computer Science and Engineering, University of California, Riverside, California, USA.
Bioinformatics. 2008 Aug 1;24(15):1733-4. doi: 10.1093/bioinformatics/btn307. Epub 2008 Jul 2.
Software applications for structural similarity searching and clustering of small molecules play an important role in drug discovery and chemical genomics. Here, we present the first open-source compound mining framework for the popular statistical programming environment R. The integration with a powerful statistical environment maximizes the flexibility, expandability and programmability of the provided analysis functions.
We discuss the algorithms and compound mining utilities provided by the R package ChemmineR. It contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of classification algorithms and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine environment and allows bidirectional communications between the two services.
ChemmineR is freely available as an R package from the ChemMine project site: http://bioweb.ucr.edu/ChemMineV2/chemminer
用于小分子结构相似性搜索和聚类的软件应用在药物发现和化学基因组学中发挥着重要作用。在此，我们为流行的统计编程环境R展示了首个开源化合物挖掘框架。与强大的统计环境集成可最大化所提供分析功能的灵活性、可扩展性和可编程性。
我们讨论了R包ChemmineR提供的算法和化合物挖掘实用工具。它包含用于结构相似性搜索的函数、使用多种分类算法对化合物库进行聚类的函数以及用于管理复杂化合物数据的各种实用工具。它还为化合物簇和化学结构提供了广泛的可视化功能。该包与在线ChemMine环境良好集成，并允许这两种服务之间进行双向通信。
ChemmineR作为一个R包可从ChemMine项目网站免费获取：http://bioweb.ucr.edu/ChemMineV2/chemminer
