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November 23, 2004
The pathways for Mandalate,
(US) or
(UK),
and 4-Nitrophenol,
(US) or
(UK),
have been updated.
Some UM-BBD users report that they can connect to the home page
of the database and other static pages, but cannot connect to a
compound page or other dynamic pages. The problem may be that
port 8015 is used to view the dynamic pages, rather than the
more usual port 80. If users have this problem, they must ask
their computer system administrator to open port 8015 for web access.
Alternatively, they can use the UM-BBD SRS mirror.
This information has been added to the UM-BBD FAQ page.
On the Useful Internet Resources page, the links for
Thermodynamics of Enzyme-Catalyzed Reactions from the National
Institute of Standards and Technology, E. coli Index from the
University of Birmingham, UK, and the Journal of Biochemistry
have been updated.
October 19, 2004
The pathways for 3,3',5,5'-Tetrabromobisphenol A,
(US) or
(UK),
and Nitrobenzene,
(US) or
(UK),
have been updated.
The Pathway Prediction System (PPS) biotransformation rules have been
revised. There are now 250 rules. A list of all rules is available.
The system can now handle 503 (80%) of the 629 pathway branches from
115 UM-BBD compounds containing C and H, O, N, P, S and/or halides
that initiate pathways containing two or more reactions.
On the Useful Internet Resources page, the links for the
National Toxicology Program and Search of NTP databases
have been updated.
September 13, 2004
A pathway for Osmium Reduction,
(US) or
(UK),
has been added
and the pathway for
Tetrahydrofuran,
(US) or
(UK),
has been updated. The Osmium pathway is the
twelfth metal, metalloid or metal chelator pathway in the
UM-BBD. A list of these is available.
Format of a BioTransformation Rule Page has been added to the About the UM-BBD page.
On the Useful Internet Resources page,
the links for the
IUBMB-Nicholson Metabolic Pathway Chart
and the American Society for Microbiology have been updated.
A new publication: Hou, B.K., Ellis, L.B.M., and Wackett, L.P. (2004)
"Encoding Microbial Metabolic Logic: Predicting Biodegradation"
Journal of Industrial Microbiology and Biotechnology, 31: 261-272,
has been added to the Publications page.
July 7, 2004
The pathways for Fluorene,
(US) or
(UK),
and Arsonate, (US) or
(UK),
have been updated.
In Biochemical Periodic Tables, a new entry was made for
Osmium (Os), and the entries for Arsenic (As), Phosphorus (P)
and Fluorine (F) were updated.
On the Useful Internet Resources page, the link for Yeast Genome Pathways at MIPS has been updated.
June 17, 2004
The pathway for Pivalic Acid (anaerobic),
(US) or
(UK),
was added and the
pathway for Perchlorate (anaerobic),
(US) or
(UK),
has been updated.
The Pivalic Acid pathway was started by a student in the 2004
Biocatalysis and Biodegradation class, offered completely over the Internet.
Links to the IntEnz Database at EBI have been added to all
enzyme pages. A searchable list of enzymes is available.
All pathway pages have been examined, and narratives have been
updated if needed. Pathways are aerobic unless otherwise specified.
Pathways that are anaerobic, all or in part, can be found by
searching pathway names for "anaerobic OR an/aerobic."
A searchable list of all pathways is available.
An About the Biochemical Periodic Tables web page has been
created. It is linked to on the About the BBD page and on the
main Biochemical Periodic Tables page.
On the Useful Internet Resources page, a link has been added for
the IntEnz: Intergrated Enzyme Database at the EBI.
May 18, 2004
The pathways for Naphthalene,
(US) or
(UK),
beta-1,2,3,4,5,6-Hexachlorocyclohexane,
(US) or
(UK),
and anaerobic Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX),
(US) or
(UK),
have been updated.
The number of hits retrieved by UM-BBD dynamic searches of
GenPept and PDB have been updated. GenPept and PDB searches
are found on many enzyme pages. A complete list of enzyme pages
is available.
On the Useful Internet Resources page, a link has been added for
the Epoxide hydrolase and haloalkane dehalogenase database at the
University of Stuttgart.
April 20, 2004
A new pathway has been added for N-Cyclohexylisocyanide,
(US) or
(UK),
and the
pathways for o-Nitrobenzoate,
(US) or
(UK),
Limonene,
(US) or
(UK),
Trifluoroacetate,
(US) or
(UK),
and
Glyphosate,
(US) or
(UK),
have been updated.
All compound graphics have been redrawn using the ChemSketch 5.0
chemical drawing package. UM-BBD reaction, mechanism and pathway
graphics are being converted as time permits. ChemSketch has been
added to the UM-BBD Tools page.
On the Useful Internet Resources page, links has been updated for
EXTOXNET and the Environmental Fate Database.
March 9, 2004
The pathways for o-Nitrobenzoate,
(US) or
(UK),
the 1,3-Dichloropropene family,
(US) or
(UK),
and
the 3-Chloroacrylic acid family
(US) or
(UK),
have been updated.
Many compound SMILES string have been corrected and the remainder
are being checked, and corrected if needed, as time permits.
SMILES strings are displayed on compound pages.
A complete list of compound pages is available.
On the Useful Internet Resources page, a link has been updated for
the Agricultural Research Service Pesticide Properties Database, and
Environmental Programs at the Lawrence Livermore National Laboratory
has been removed.
February 18, 2004
The pathways for methyl-tert-butylether
(US) or
(UK),
and chlorobenzene
(US) or
(UK),
have been updated.
A mechanism graphic was drawn for the quercetin 2,3-dioxygenase
reaction in the quercetin pathway, bringing to 31 the number
of such graphics. A list of these is available.
In Biochemical Periodic Tables, a new entry was made for
Radium (Ra), and the entries for Thorium (Th) and Bismuth (Bi)
were updated.
A new publication is available on the UM-BBD Publications Page:
Wackett, L.P., Dodge, A.G., and Ellis, L.B.M. (2004) "Microbial
Genomics and the Periodic Table" (minireview)
Applied and Environmental Microbiology, 70: 647-65.
On the Useful Internet Resources page, a link has been added to
the IUBMB-Nicholson Metabolic Pathway Chart.
January 20, 2004
A pathway for phenylboronic acid,
(US) or
(UK),
has been added.
A mechanism graphic was drawn for the phenylboronic acid monooxygenase
reaction in the phenylboronic acid pathway, bringing to 30 the number
of such graphics. A list of these is available.
In Biochemical Periodic Tables, the entry for Boron (B) has been updated.
Registration has closed for the 2004 offering of
Biocatalysis and Biodegradation, a University of Minnesota class
offered completely over the Internet, and the class has started.
The What's New page restarts; 2003 activities have been archived.
2003 Archives
2002 Archives
2001 Archives
2000 Archives
1999 Archives
1998 Archives
1997 Archives
1996 Archives
1995 Archives
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