Cell2Chem: mining explored and unexplored biosynthetic chemical spaces.

Bioinformatics
Dongliang LiuQian-Nan Hu

Abstract

Living cell strains have important applications in synthesizing their native compounds and potential for use in studies exploring the universal chemical space. Here, we present a web server named as Cell2Chem which accelerates the search for explored compounds in organisms, facilitating investigations of biosynthesis in unexplored chemical spaces. Cell2Chem uses co-occurrence networks and natural language processing to provide a systematic method for linking living organisms to biosynthesized compounds and the processes that produce these compounds. The Cell2Chem platform comprises 40 370 species and 125 212 compounds. Using reaction pathway and enzyme function in silico prediction methods, Cell2Chem reveals possible biosynthetic pathways of compounds and catalytic functions of proteins to expand unexplored biosynthetic chemical spaces. Cell2Chem can help improve biosynthesis research and enhance the efficiency of synthetic biology. Cell2Chem is available at: http://www.rxnfinder.org/cell2chem/.

References

Jun 9, 2012·PloS One·Chih-Hsuan WeiZhiyong Lu
Mar 27, 2015·Journal of Cheminformatics·Robert LeamanZhiyong Lu
Sep 25, 2015·Nucleic Acids Research·Sunghwan KimStephen H Bryant
Oct 16, 2015·Nucleic Acids Research·Janna HastingsChristoph Steinbeck
Oct 17, 2015·Bioinformatics·Weizhong TuQian-Nan Hu
Mar 12, 2016·Cell·Jens Nielsen, Jay D Keasling
Jul 28, 2017·PloS One·Christian-Alexander DudekDietmar Schomburg
Oct 12, 2018·Bioinformatics·Le YuanQian-Nan Hu
May 23, 2019·Nucleic Acids Research·Chih-Hsuan WeiZhiyong Lu

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