University of Minnesota Biocatalysis/Biodegradation Database
                  Progress Report 95 - March 20, 2002

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- Pathways for the biodegradation of 1,2,3,4-tetrachlorobenzene, 
  and Mordant Yellow 3 have been added, and the pathway for propylene
  has been updated.  The 1,2,3,4-tetrachlorobenzene and Mordant Yellow 3
  pathways were developed by students in the 2001 Biocatalysis and 
  Biodegradation class offered completely over the Internet.  The 
  Mordant Yellow 3 pathway includes another reaction of the versatile
  enzyme, naphthalene 1,2-dioxygenase, bringing to 76 the number of 
  reactions known for this enzyme.  A list of these is available.
  http://umbbd.ahc.umn.edu/tcb/tcb_map.html
  http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[upathway-id:'tcb_map']
  http://umbbd.ahc.umn.edu/my3/my3_map.html
  http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[upathway-id:'my3_map']
  http://umbbd.ahc.umn.edu/pro/pro_map.html
  http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[upathway-id:'pro_map']
  http://www.cbs.umn.edu/class/bioc/5309/idl/
  http://umbbd.ahc.umn.edu/naph/ndo.html

- Structure-based searching has been added to the UM-BBD.
  Enter the SMILES string of the compound you wish to search
  for, the type of structure search (similarity, substructure or exact)
  you wish to do, and the similarity threshold to use.  Images of
  matching structures in the UM-BBD are returned. Clicking on the image
  of a returned compound leads to the corresponding UM-BBD compound 
  page, and from there to reactions of and biodegradation pathways 
  for the compound.  This is the first step towards predicting a 
  biodegradation pathway for compounds the UM-BBD does not contain.
  The biodegradation pathways for UM-BBD compounds that are similar
  to the query compound can suggest ways the query might be degraded.
  This structure search is linked to on the main search page.  
  It is based on the JChem toolkit from ChemAxon, Ltd., listed on 
  the UM-BBD Tools page.
  http://umbbd.ahc.umn.edu/search/ssmiles.html
  http://umbbd.ahc.umn.edu/search/index.html
  http://umbbd.ahc.umn.edu/tools.html

If you have comments on any aspect of the UM-BBD, please let us know.
         
Lynda Ellis <[log in to unmask]>