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Systems chemical biology

The increasing availability of data related to genes, proteins and their modulation by small molecules has provided a vast amount of biological information leading to the emergence of systems biology and the broad use of simulation tools for data analysis. However, there is a critical need to develop cheminformatics tools that can integrate chemical knowledge with these biological databases and simulation approaches, with the goal of creating systems chemical biology.

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Figure 1: A simplified representation of the glyoxylate pathway, extracted from KEGG.
Figure 2: Conceptual representation of the systems chemical biology approach, applied to the glyoxylate pathway.

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Acknowledgements

This work was supported in part by the NIH grant U54 MH074425-01 (T.I.O.) and by the NIH planning grant P20-HG003898 (A.T.). Sandia is operated by Sandia Corporation, a Lockheed Martin Company, for the US Department of Energy under Contract DE-AC04-94AL85000 (J.-L.F. and M.D.R.). The authors express their gratitude to T.K. Allu and D.C. Fara (University of New Mexico) for the PubChem bioassay data analysis.

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T.I.O. is the founder and CEO of Sunset Molecular Discovery LLC, which markets small-molecule databases for the pharmaceutical industry. He also serves on the Scientific Advisory Board for ChemDiv, Inc., and he owns stock in AstraZeneca plc.

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Oprea, T., Tropsha, A., Faulon, JL. et al. Systems chemical biology. Nat Chem Biol 3, 447–450 (2007). https://doi.org/10.1038/nchembio0807-447

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