Le Yuan1,2,3, Yu Tian1,3, Shaozhen Ding2, Yanfang Liu1,3, Fu Chen1,4, Tong Zhang1,4, Weizhong Tu5, Junni Chen5, Qian-Nan Hu2. 1. Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, P. R. China. 2. CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences Chinese Academy of Sciences, Shanghai, P. R. China. 3. University of Chinese Academy of Sciences, Beijing, P. R. China. 4. College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P. R. China. 5. Wuhan LifeSynther Science and Technology Co. Limited, Wuhan, P. R. China.
Abstract
SUMMARY: Synthetic biology has a great potential to produce high value pharmaceuticals, commodities or bulk chemicals. However, many biosynthetic target molecules have no defined or predicted biosynthetic pathways. Biosynthetic precursors are crucial to create biosynthetic pathways. Thus computer-assisted tools for precursor identification are urgently needed to develop novel metabolic pathways. To this end, we present PrecursorFinder, a computational tool that explores biosynthetic precursors for the query target molecules using chemical structure, similarity as well as MCS (maximum common substructure). This platform comprises more than 60 000 compounds biosynthesized for being promising precursors, which are extracted from >500 000 scientific literatures and manually curated by more than 100 people over the past 8 years. The PrecursorFinder could speed up the process of biosynthesis research and make synthetic biology or metabolic engineering more efficient. AVAILABILITY AND IMPLEMENTATION: PrecursorFinder is available at: http://www.rxnfinder.org/precursorfinder/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Synthetic biology has a great potential to produce high value pharmaceuticals, commodities or bulk chemicals. However, many biosynthetic target molecules have no defined or predicted biosynthetic pathways. Biosynthetic precursors are crucial to create biosynthetic pathways. Thus computer-assisted tools for precursor identification are urgently needed to develop novel metabolic pathways. To this end, we present PrecursorFinder, a computational tool that explores biosynthetic precursors for the query target molecules using chemical structure, similarity as well as MCS (maximum common substructure). This platform comprises more than 60 000 compounds biosynthesized for being promising precursors, which are extracted from >500 000 scientific literatures and manually curated by more than 100 people over the past 8 years. The PrecursorFinder could speed up the process of biosynthesis research and make synthetic biology or metabolic engineering more efficient. AVAILABILITY AND IMPLEMENTATION: PrecursorFinder is available at: http://www.rxnfinder.org/precursorfinder/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.