University of Minnesota Biocatalysis/Biodegradation Database
                   Progress Report 151 - June 27, 2007

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- Links to Medline primary references on reaction pages and in
   Biochemical Periodic Table element pages now use the PubMed
   AbstractPlus format.  For example, see the link to the Medline
   reference in the Atrazine to Hydroxyatrazine reaction page.
   A list of all reactions is available.
   http://umbbd.msi.umn.edu/periodic/
   http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=r0113
   http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allreacs

- In the Biochemical Periodic Tables, the element page for Sulfur
   has been updated.
   http://umbbd.msi.umn.edu/periodic/elements/s.html

- In the Pathway Prediction System (PPS), relative reasoning
   has been implemented.  This allows rules for biotransformation
   to have relative likelihoods among themselves in addition to their
   absolute aerobic likelihood.  Relative likelihood is based
   on metabolic logic and study of the biotransformations of all
   UM-BBD compounds, comparing those a compound can undergo
   to those it is known to undergo in the UM-BBD.  As implemented
   in the PPS, biotransformations with lower relative likelihood are
   removed from the list of choices. To demonstrate this feature,
   two relative rules "ring cleavage > ring di- and mono-oxygenation"
   and "hydroxyaromatic ring vic-monooxygenation > ring dioxygenation
   and other position monooxygenation," were implemented.  PPS
   predictions for aromatic compounds have increased specificity,
   with no loss in sensitivity.  Try it using the PPS demo compound,
   benzyl alcohol.
   http://umbbd.msi.umn.edu/predict/
http://umbbd.msi.umn.edu/servlets/predict.jsp?bt=aerobic&query=OCc1ccccc1

- s-Triazines are an important class of pesticide chemicals.
   The UM-BBD has focused on these compounds since its very
   beginning; the pathway map for the s-triazine atrazine was one
   of the first four in the original, February 1995, UM-BBD.
   It has been updated several times since then.  In 1999, the
   s-Triazine Metapathway Map was developed, to emphasize the similar
   biodegradation pathways found for several commercially important
   s-triazines.  Most recently, PPS predictions for this class of
   compounds have been improved.  To help publicize this project,
   a web page for 33 agricultural s-Triazines has been developed.
   Try it! A click on the SMILES string of one of the compounds,
   sends that string to the PPS, where you can generate a
   PPS-predicted biodegradation pathway for it.
   http://umbbd.msi.umn.edu/atr/atr_map.html
   http://umbbd.msi.umn.edu/tria/tria_map.html
   http://umbbd.msi.umn.edu/predict/tria.html

- On the Links page, links were added to Alan Wood's Compendium of
   Pesticide Common Names, and the IUPAC Goldbook: Compendium
   of Chemical Terminology.
   http://umbbd.msi.umn.edu/resources.html

If you have comments on any aspect of the UM-BBD, please let us know.

Lynda Ellis <[log in to unmask]>