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Home | Seminars and Symposia | Past seminars/symposia: Friday, September 29, 2006

Computational Prediction of Chemical Fate in the Environment

by

Lawrence P. Wackett
Department of Biochemistry, Molecular Biology
and Biophysics, and Biotechnology Institute,
University of Minnesota

Friday, September 29, 2006
12:00 Lunch
12:15 Seminar

402 Walter Library

Download slides (pdf 1.4 MB) Over 18 million chemical compounds are known, with more than 65,000 currently used in commerce. Though the fate and longevity of chemicals in the environment is largely predicated on their biodegradation by microbes, this ability has been determined for only a small percentage of these chemicals. To fill the gap and because compounds may have more toxic metabolites, there is increasing interest in using computational methods to predict microbial biodegradation pathways. The prediction tool was developed using information contained within the University of Minnesota Biocatalysis/Biodegradation Database1 (UM-BBD, http://umbbd.msi.umn.edu/). The UM-BBD provides curated information on over 1000 microbial catabolic reactions, emphasizing the breadth of known biochemical reaction types. The different biochemical reaction types were represented in a set of approximately 250 computational rules. The rules are applied to computationally metabolize any organic chemical compound via the Pathway Prediction System (PPS).2 This generated many possible metabolic pathways. Users from industry and regulatory agencies requested that we develop a knowledge-based system to predict which metabolic pathways are most likely to determine the fate of chemicals in the environment.3

References

  1. L.B.M. Ellis, D. Roe, and L.P. Wackett (2006) “The University of Minnesota Biocatalysis/Biodegradation Database: The first decade,” Nucl. Acids Res. 34: D517-D521.
  2. B.K. Hou, L.P. Wackett, and L.B.M. Ellis (2003) “Microbial pathway prediction: A functional group approach,” J. Chem. Inf. Comp. Sci. 43:1051-1057.
  3. Predict-BT website, URL = http://umbbd.msi.umn.edu/predictbt/.