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Subject:
From:
Lynda Ellis <[log in to unmask]>
Reply To:
University of Minnesota Biocatalysis/Biodegradation Database <[log in to unmask]>
Date:
Fri, 18 Apr 2008 10:44:03 -0500
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TEXT/PLAIN
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       University of Minnesota Biocatalysis/Biodegradation Database
                   Progress Report 161 - April 18, 2008

Thank you for your interest in the UM-BBD.

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- A pathway for the aerobic Phenol Family has been added. This includes
   metabolism for phenol, phenylboronic acid, and diphenyl ether.
   http://umbbd.msi.umn.edu/pba/pba_map.html
   http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[upathway-id:'pba_map']

- Two additional super rules, rules that include two or more contiguous
   btrules that form a small pathway of their own, have been added to
   the Pathway Prediction System (PPS).  The first one is for angular
   dioxygenation of polynuclear aromatic compounds bridged by an ether,
   amine, or carbonyl. Test this with benzofuran, c1ccc2c(c1)oc3ccccc23,
   which goes to 2,2',3-trihydroxybiphenyl in one step using the super
   rule bt0374.  The second one is for degradation of 2,4,6-trinitrophenol
   (picric acid) and 2,4-dinitrophenol.  Try this out by pasting
   Picric acid, [O-]c1c(cc(cc1[N+]([O-])=O)[N+]([O-])=O)[N+]([O-])=O
   into the PPS SMILE string box.  It is transformed to
   2,4-dinitrocyclohexanone in one step using the super rule bt0378.
   Predictions for these classes of compounds are better and faster.
   http://umbbd.msi.umn.edu/predict/
   http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=bt0374 
http://umbbd.msi.umn.edu/servlets/predict.jsp?bt=aerobic&query=c1ccc2c(c1)oc3ccccc23
   http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=bt0378

- Relative reasoning, giving one btrule priority over another, was
   announced last June.  Now a list of all btrules using it, and which
   rules each has priority over, is available.  It is linked to on the
   list of all rules and the main search and browse page.
   http://umbbd.msi.umn.edu/cgi-bin/relative_reasoning.cgi
   http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allrules
   http://umbbd.msi.umn.edu/search/

- Due to changes in the ATCC website, links to ATCC no longer
   work.  We will be moving UM-BBD microorganism links to the
   WFCC-MIRCEN World Data Centre for Microorganisms.  This change
   has been made on the list of microorganisms, and will be made
   on pathway map pages as time permits.
   http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allmicros

- On the Links page, a link was added for IPCS INCHEM: Chemical
   Safety Information from Intergovernmental Organizations, and a
   link was updated for the WFCC-MIRCEN World Data Centre for
   Microorganisms.
   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]>

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