University of Minnesota Biocatalysis/Biodegradation Database
Progress Report 134 - December 19, 2005
Email list problems starting in July, 2005 meant that some of our email
list members did not receive the messages sent to the list from then to
now.
Thus we are now resending the four progress reports sent since that time.
We apologize for any duplicate progress reports you may receive.
For this and other reasons, we have moved to a new email list server.
This move should be transparent to the UM-BBD email list members.
To subscribe, unsubscribe, or change your subscription options, go to:
http://lists.umn.edu/cgi-bin/wa?SUBED1=um-bbd&A=1
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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University of Minnesota Biocatalysis/Biodegradation Database
Progress Report 133 - November 23, 2005
- A pathway for fosfomycin was added. This pathway was
developed by a student in the 2005 BioC/MicE 5309 class.
http://umbbd.ahc.umn.edu/ffm/ffm_map.html
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[upathway-id:'ffm_map']
- The minireview: Lawrence P. Wackett, Anthony G. Dodge, Lynda B. M. Ellis
(2004) "Microbial Genomics and the Periodic Table" Applied and
Environmental Microbiology 70: 647-655, is one of the AEM's "Top 20"
most requested articles, July - September 2005.
http://umbbd.ahc.umn.edu/publications/
http://aem.asm.org/misc/Top_20.shtml
- On the Useful Internet Resources page, the link for
PROCAT was replace by the Catalytic Site Atlas, at EMBL-EBI
http://umbbd.ahc.umn.edu/resources.html
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University of Minnesota Biocatalysis/Biodegradation Database
Progress Report 132 - October 21, 2005
- A pathway for the nylon oligomer was added. This pathway was
developed by a student in the 2005 BioC/MicE 5309 class.
http://umbbd.ahc.umn.edu/nyl/nyl_map.html
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[upathway-id:'nyl_map']
- The Pathway Prediction System (PPS) web-based tutorial is now
also available in a printer-friendly .pdf version.
http://umbbd.ahc.umn.edu/predict/aboutPPS.html
http://umbbd.ahc.umn.edu/predict/PPStutorial.pdf
- The UM-BBD was featured in Netwatch section of Science: Leslie, Mitch
(2005) "DATABASE: Eating Pollution" Netwatch, Science, 309: 1795.
This and other reviews and publications are found on our Publications
page.
http://umbbd.ahc.umn.edu/publications/
- On the Useful Internet Resources page, the link for
Lignin Biodegradation by White Rot Fungi has been deleted.
http://umbbd.ahc.umn.edu/resources.html
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University of Minnesota Biocatalysis/Biodegradation Database
Progress Report 131 - September 12, 2005
- Further implementation of suggestions made at the PredictBT workshop
held May 6-7, 2005: Now the Pathway Prediction System (PPS) indicates
the predicted compounds found in the UM-BBD. The "Cpd" button is
that indicator. It links to the compound page, and from there to
reaction and pathway information. More information on the PPS,
including the Cpd button, is found in "About the PPS."
http://umbbd.ahc.umn.edu/workshop2/
http://umbbd.ahc.umn.edu/predict/
http://umbbd.ahc.umn.edu/predict/aboutPPS.html
- We are moving PPS biotransformation rules to ChemAxon's Reactor
system as time permits. The rules that have been moved now
display images of their patterns on their btrule pages.
For example, see bt0005,
vic-unsubstituted Benzenoid -> cis-Dihydroxydihydrobenzenoid.
The format of the btrule page is described in "About the BBD."
http://www.chemaxon.com/products.html#Reactor
http://umbbd.ahc.umn.edu:8015/umbbd/rule.jsp?rule=bt0005
http://umbbd.ahc.umn.edu/aboutBBD.html
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University of Minnesota Biocatalysis/Biodegradation Database
Progress Report 130 - August 17, 2005
- A pathway for Branched-Chain Dodecylbenzene Sulfonate was added.
This pathway was developed by a student in the 2005 BioC/MicE 5309
class.
http://umbbd.ahc.umn.edu/bcds/bcds_map.html
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[upathway-id:'bcds_map']
- Further implementation of suggestions made at the PredictBT workshop
held May 6-7, 2005: Now the Pathway Prediction System (PPS) shows the
aerobic likelihood scores assigned at that workshop as a color bar
to the left of each predicted compound.
http://umbbd.ahc.umn.edu/workshop2/
http://umbbd.ahc.umn.edu/predict/
- An About the PPS web page has been created that describes the PPS,
including the new color bar, in more detail.
http://umbbd.ahc.umn.edu/predict/aboutPPS.html
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