What's New in the UM-BBD?
April 18, 2008
A pathway for the aerobic Phenol Family,
(US) or
(UK),
has been added. This includes
metabolism for phenol, phenylboronic acid, and diphenyl ether.
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.
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.
Due to changes in the ATCC website, our links to ATCC no longer
work. We are 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.
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.
March 19, 2008
A pathway for N-nitrosodimethylamine,
(US) or (UK),
has been added, and the
pathways for the picric acid family,
(US) or (UK),
and the naphthalene sulfonate family,
(US) or (UK),
have been updated. The pathway for N-Nitrosodimethylamine
was started by a student in the 2007 BioC/MicE 5309 class.
In the Pathway Prediction System (PPS), prediction of oxidation
of a secondary carbon (bt0242), and addition of water to a double
bond (bt0021), have been improved.
Lhasa Limited is developing
MEPPS, a new expert knowledge base
software project for the prediction of microbial degradation in
the environment. It is a stand-alone, PC-based system, combining
data from the UM-BBD Pathway Prediction System with expert
reasoning software from Lhasa. There are openings for sponsors
for further development of MEPPS. For more information on MEPPS,
or if you are interested in helping to sponsor this new and
exciting project, contact Sian Ives <Sian.Ives@lhasalimited.org>.
Students in our 2008 BioC/MicE 5309 Biocatalysis and Biodegradation
class, offered completely over the Internet, have examined websites
on the UM-BBD Links page and selected the ones of most interest to
them. The Links page now links to the list of these choices and the
reason each site was selected.
February 15, 2008
A pathway for endosulfan, a chlorinated pesticide,
(US) or (UK),
has been added,
and the pathway for phthalate,
(US) or (UK),
has been updated. The pathway for
endosulfan was started by a student in the 2007 BioC/MicE 5309 class.
Structure-based variable aerobic likelihood has been added to the
Pathway Prediction System (PPS). For aerobically likely aromatic
ring monooxygenation, ring dioxygenation, ring cleavage, and
ring decarboxylation rules, when the substrate contains one or more
halogens, the aerobic likelihood for the transformation is changed
to "neutral". This is the first step toward better handling of
aerobic likelihood. Test it by comparing intradiol cleavage
(bt0254) of catechol,
Oc1c(O)cccc1, with that of
tetrachlorocatechol,
Oc1c(O)c(Cl)c(Cl)c(Cl)c1(Cl). The same
pathway is predicted, but the one for catechol is aerobically
likely and the one for tetrachlorocatechol is aerobically neutral.
The International Advisory Board for the UM-BBD and PPS has been
updated. Continuing members: Philip Judson, Lhasa Limited; Sol Resnick, Dow
Chemicals. New members: Bob Boethling, EPA; Kathrin Fenner, EAWAG;
Stefan Kramer, Technical University of Munich (TUM).
On the Links page, a link was added for the Online Chemical Database,
and a link was updated for ZINC, from UCSF.
January 23, 2008
The pathway for nicotine,
(US) or (UK),
has been updated.
The scrollable list of pathways on the UM-BBD home page is now so large
that it has been reformatted for better user access.
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).
These are for the first and second
steps in cleavage of pyridines and nicotines and their derivatives.
Predictions for this class of compounds are better and faster.
Try out these super rules using pyridine-2-carboxamide (picolinamide),
a photolytic product of the herbicide Diquat, C1=CC=NC(=C1)C(=O)N.
The amide is first removed to form 2-carboxypyridine, which is cleaved
to 2,5-dihydroxypyridine using the first super rule (bt0362). The latter is cleaved to
fumarate and acetoacetate using the second (bt0363). Prediction of
decarboxylation (bt0051 and bt0082) have also been improved.
In a PPS prediction, when the Next button will take you to a readily degraded
compound that will end a prediction, that button is now shaded green.
You can chose it to end the prediction, or continue the prediction by
choosing a non-green Next button. This is described in more detail
in the About the PPS tutorial.
On the Links page,
links were added to BDPServer: prediction of
environmental fate for chemical compounds, National Center for
Biotechnology, Spain, and BiocatCollection: International Collection of Biocatalysts.
The link for MetaRouter was removed.
The What's New page restarts; 2007 activities have been archived.
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