Vogt Martin, Stumpfe Dagmar, Maggiora Gerald M, Bajorath Jürgen
Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, 53113, Bonn, Germany.
BIO5 Institute, University of Arizona, 1657 East Helen Street, Tucson, AZ, 85721, USA.
J Comput Aided Mol Des. 2016 Mar;30(3):191-208. doi: 10.1007/s10822-016-9906-3. Epub 2016 Mar 5.
The concept of chemical space is of fundamental relevance in chemical informatics and computer-aided drug discovery. In a series of articles published in the Journal of Computer-Aided Molecular Design, principles of chemical space design were evaluated, molecular networks proposed as an alternative to conventional coordinate-based chemical reference spaces, and different types of chemical space networks (CSNs) constructed and analyzed. Central to the generation of CSNs was the way in which molecular similarity relationships were assessed and a primary focal point was the network-based representation of biologically relevant chemical space. The design and comparison of CSNs based upon alternative similarity measures can be viewed as an evolutionary path with interesting lessons learned along the way. CSN design has matured to the point that such chemical space representations can be used in practice. In this contribution, highlights from the sequence of CSN design efforts are discussed in context, providing a perspective for future practical applications.
化学空间的概念在化学信息学和计算机辅助药物发现中具有根本的相关性。在发表于《计算机辅助分子设计杂志》的一系列文章中，评估了化学空间设计的原则，提出了分子网络作为传统基于坐标的化学参考空间的替代方案，并构建和分析了不同类型的化学空间网络（CSN）。CSN生成的核心是评估分子相似性关系的方式，一个主要焦点是基于网络的生物学相关化学空间表示。基于替代相似性度量的CSN设计和比较可被视为一条具有沿途有趣经验教训的进化路径。CSN设计已经成熟到可以在实践中使用这种化学空间表示的程度。在本论文中，将结合上下文讨论CSN设计工作序列中的要点，为未来的实际应用提供一个视角。
