Improving Biodegradation Pathway Prediction

by

Lynda B.M. Ellis
Laboratory Medicine and Pathology
University of Minnesota

Friday, October 17, 2008
12:00 lunch
12:15 seminar
402 Walter Library

The University of Minnesota Pathway Prediction System (UM-PPS, http://umbbd.msi.umn.edu/predict/) recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions, and predicts transformations of these groups based on biotransformation rules. Rules are based on the University of Minnesota Biocatalysis/Biodegradation Database (http://umbbd.msi.umn.edu/) and the scientific literature. As rules were added to the UM-PPS, more were triggered at each prediction step. The resulting combinatorial explosion is being addressed in four ways. Biodegradation experts give each rule an aerobic likelihood value of Very Likely, Likely, Neutral, Unlikely, or Very Unlikely. Users now can choose whether they view all, or only the more aerobically likely, predicted transformations. Relative reasoning, allowing triggering of some rules to inhibit triggering of others, was implemented. Rules were originally assigned to individual chemical reactions. In selected cases, these have been replaced by super rules, which include two or more contiguous reactions that form a small pathway of their own. Rules are continually modified to improve the prediction accuracy; increasing rule stringency can improve predictions and reduce extraneous choices. The UM-PPS is freely available to all without registration. Its value to the scientific community, for academic, industrial, and government use, is good and will only increase.

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