Nucleic Acids Research Advance Access originally published online on June 4, 2008
Nucleic Acids Research 2008 36(Web Server issue):W427-W432; doi:10.1093/nar/gkn315
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W427-W432
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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The University of Minnesota pathway prediction system: predicting metabolic logic
1Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA, 2Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, CH-8092 Zürich, 3Swiss Federal Institute for Aquatic Science and Technology (Eawag), CH-8600 Dübendorf, Switzerland and 4Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN 55108, USA
*To whom correspondence should be addressed. Tel: +1 612 635 9122; Fax: +1 612 624 6404; Email: lynda{at}umn.edu
Received January 24, 2008. Revised April 17, 2008. Accepted May 7, 2008.
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 of them 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 initially 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 In selected cases, these have been replaced by super rules, which include two or more contiguous reactions that form a small pathway of their own.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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