Weber Tilmann, Kim Hyun Uk
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark.
BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
Synth Syst Biotechnol. 2016 Feb 5;1(2):69-79. doi: 10.1016/j.synbio.2015.12.002. eCollection 2016 Jun.
Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other 'omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work. In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on 'omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http://www.secondarymetabolites.org) is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.
天然产物是药物发现中先导分子的最重要来源之一。随着经济实惠的全基因组测序技术和其他“组学”工具的发展，天然产物研究领域目前正在经历范式转变。几十年来，主要是分析和化学方法使人们能够获取这类化合物，如今基于基因组学的方法为寻找、鉴定和表征此类分子提供了补充方法。这种范式转变也导致对计算工具的高需求，以协助研究人员开展日常工作。在此背景下，本综述总结了目前可用于基于“组学”数据挖掘、鉴定和表征天然产物生物合成途径及其生产者的工具和数据库。介绍了一个名为次生代谢物生物信息学门户（网址为http://www.secondarymetabolites.org的SMBP）的门户网站，以提供一站式目录以及指向这些生物信息学资源的链接。此外，还展望了现有工具和即将开发的工具将如何影响天然产物领域的合成生物学方法。
