The University of Minnesota pathway prediction system: predicting metabolic logic.
The University of Minnesota pathway prediction system: predicting metabolic logic.
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DOI：
10.1093/nar/gkn315
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发表时间：
2008-07-01
影响因子：
14.9
通讯作者：
Wackett LP
中科院分区：
文献类型：
--
作者：
Ellis LB;Gao J;Fenner K;Wackett LP
明尼苏达大学途径预测系统（UM-PPS，http://umbbd.msi.umn.edu/predict/）识别有机化合物中作为微生物分解代谢反应的潜在目标的官能团，并根据生物转化规则预测这些基团的转化。规则基于明尼苏达大学生物催化/生物降解数据库 (http://umbbd.msi.umn.edu/) 和科学文献。随着规则添加到 UM-PPS，每个预测步骤都会触发更多规则。由此产生的组合爆炸正在通过四种方式得到解决。生物降解专家为每条规则赋予了“非常可能”、“可能”、“中性”、“不太可能”或“非常不可能”的有氧可能性值。用户现在可以选择是查看所有预测的转变，还是仅查看更有氧可能性的预测转变。实现了相对推理，允许触发某些规则以抑制其他规则的触发。规则最初被分配给各个化学反应。在某些情况下，这些已被超级规则所取代，其中包括两个或多个连续的反应，形成自己的小路径。规则不断修改，提高预测精度；增加规则的严格性可以改善预测并减少无关的选择。 UM-PPS 可供所有人免费使用，无需注册。它对科学界、学术界、工业界和政府的价值是良好的，而且只会增加。
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 In selected cases, these have been replaced by super rules, which include two or more contiguous reactions that form a small pathway of their own.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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影响因子：
14.9
作者：
Ellis LB;Roe D;Wackett LP
通讯作者：
Wackett LP
影响因子：
3
作者：
Dimitrov, S;Kamenska, V;Mekenyan, O
通讯作者：
Mekenyan, O
影响因子：
8.8
作者：
Gerecke, Andreas C.;Giger, Walter;Kohler, Martin
通讯作者：
Kohler, Martin
DOI：
10.1021/ci0202739
发表时间：
2003-09-01
期刊：
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
影响因子：
--
作者：
Button, WG;Judson, PN;Vessey, JD
通讯作者：
Vessey, JD
DOI：
10.1021/ci034018f
发表时间：
2003-05-01
期刊：
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
影响因子：
--
作者：
Hou, BK;Wackett, LP;Ellis, LBM
通讯作者：
Ellis, LBM