What's New in the UM-BBD?

December 29, 2006
An anaerobic pathway for 2-methylnaphthalene, (US) or (UK), has been added. This pathway was developed by a student in the 2006 BioC/MicE 5309 class. On the UM-BBD Pathway Prediction System (PPS), rule patterns now show aerobic likelihood values. At present these are identical to the parent rule values, but in the future likelihoods may differ for different patterns for the same rule. For example, see bt0291, Alkene -> Alkane, and all its patterns.

November 27, 2006
Pathways for thioacetamide, (US) or (UK), and thiobenzamide, (US) or (UK), have been added. On UM-BBD Pathway Prediction System (PPS), the internal method used to store information between PPS prediction steps has changed. Predictions may be faster, more stable, and the PPS may permit longer predicted pathways.

November 6, 2006
Pathways for geraniol, (US) or (UK), and citronellol, (US) or (UK), have been added. The these pathways were developed by students in the 2006 BioC/MicE 5309 class. On UM-BBD Pathway Prediction System (PPS), predicted pathway compound applets now include buttons for the btrule that produced them, and when possible, a link to the UM-BBD compound page for that compound. Information on the system is available on the About the PPS page. On the Links page, the links to PathDB at NCGR, and 1997 Student Papers at U Wisconsin, Eau Claire, have been deleted.

September 28, 2006
A pathway for tetralin, (US) or (UK), has been added. The tetralin pathway was developed by students in the 2005 and 2006 BioC/MicE 5309 class. On UM-BBD reaction pages, the number of hits from Medline searches have been updated. On UM-BBD enzyme pages, the sensitivity and specificity of GenBank, GenPept, and PDB searches have been improved, and a link to the Enzyme Database at Trinity College, Dublin, has been added to all enzymes that have 4-digit EC codes. Lists of all reaction pages and all enzyme pages are available. On UM-BBD compound pages, links to molecular models have been removed. Molecular models of all UM-BBD compounds are now available from PubChem, by following the PubChem Substance Entry link on each compound page. Compound information is downloadable at the bottom of each PubChem Substance (and Compound) Entry. A list of all compound pages is available. On the Links page, a link to the Enzyme Database at Trinity College, Dublin has been added.

August 25, 2006
A pathway for thiophene-1-carboxylate, (US) or (UK), has been added, and the pathway for beta-1,2,3,4,5,6-hexachlorocyclohexane, (US) or (UK), has been updated. The thiophene-1-carboxylate pathway was developed by a student in the 2006 BioC/MicE 5309 class. In the Pathway Prediction System, predicted pathway compounds are now separated by arrows colored with the aerobic likelihood of the relevant biotransformation rule. More information is available in About the PPS web page. UM-BBD compounds have been added to PubChem, the NCBI chemical database. A link to the UM-BBD PubChem substance entry is now available on UM-BBD compound pages. The PubChem chemical entry, found from the CID or Parent CID link on a PubChem substance entry, has even more information. The updated format of the compound page is described in About the BBD. For example, see the 1,2-dichloroethane page. On the Links page, a link to MetaCyc Biodegradation Pathways has been added and the links for DSMZ Bacterial Nomenclature Up-To-Date and IUBMB-Nicholson Metabolic Maps, Minimaps and Animaps have been updated.

August 4, 2006
Pathways for 4-Fluorobenzoate (US) or (UK), and 3-Fluorobenzoate (US) or (UK), have been added. These pathways were developed by students in the 2006 BioC/MicE 5309 class. In the Pathway Prediction System, predicted compounds are now ordered by aerobic likelihood, and loops (e.g., enol->keto->enol) have been eliminated. More information is available in About the PPS web page. Search results now include a new search form. PDB searches are again available on enzyme pages. They now search the NCBI Structures database, updated monthly from the PDB, which no longer supports search URLs. Also, the number of hits returned from GenBank, GenPept and PDB searches have been updated. For example, see the enzyme page for haloalkane dehalogenase. On the Links page, the links for DBCAT at INFOBIOGEN has been removed, and a link has been added for PGD: The Plasmid Genome Database, from the Centre of Ecology and Hydrology-Oxford, UK.

June 15, 2006
The pathway for anthracene, (US) or (UK), has been added. This pathway was started by a student in the 2005 BioC/MicE 5309 class. With the addition of this pathway, the UM-BBD now contains over 1000 biotransformation reactions of interest to the biotechnology community, an important milestone. A list of all reactions is available. All btrules that involve Coenzyme A have been rewritten to compress it to "CoA" rather than show its full structure. Graphics for those rules are now easier to read. For example, bt0094, Carboxylate + CoASH -> CoA thioester. On the Links (formerly Useful Internet Resources) page, the links for Scorecard: The Pollution Site and Scorecard Chemical Profiles were added, and the link for National Safety Council Chemical Backgrounders was updated.

May 17, 2006
The UM-BBD has a new URL: http://umbbd.ethz.ch/. The old URL will work for a while, but please update bookmarks and links soon. This move is concurrent with our move to a faster, more stable server hosted by the University of Minnesota's Supercomputing Institute. UM-BBD need for non-standard ports has been eliminated. Now all UM-BBD web pages are served from standard port 80. This should improve access behind firewalls. Top-level UM-BBD web pages have been redesigned to improve navigation. Contact us regarding server speed, standardized port, web design, or any other aspect of the UM-BBD.

April 24, 2006
The pathway for the C1 cycle, (US) or (UK), has been updated. Sol Resnick, The Dow Chemical Company, has been added to the UM-BBD International Scientific Advisory Board. The Pathway Prediction System now colors all atoms in its compounds in black. This was a suggestion of the Third PredictBT Workshop, held Dec 1-2, 2005 in Brussels, Belgium; further workshop suggestions will be implemented as time permits. All btrules have been moved to the ChemAxon Reactor system. Rules have been examined and updated during the change, and more changes are planned. All btrule pages now show their pattern graphics. A list of all rules is available. On the Links page (formerly Useful Internet Resources), a link was updated for the Agricultural Research Service Pesticide Properties Database, and a link was removed for Bioremediation Resources from the National Agricultural Library.

February 27, 2006
A pathway for benz(a)pyrene, (US) or (UK), has been added. This pathway was started by a student in the 2005 BioC/MicE 5309 class. This is the 150th pathway added to the UM-BBD, an important milestone. Dynamic searches of the Protein Data Base (PDB) have been removed from UM-BBD enzyme pages, due to problems with PDB's new web server. PDB is working to solve the problem and we will reinstall them when it is fixed. Format of all UM-BBD web pages is described in the About BBD page. The UM-BBD celebrates its birth this month. It first appeared upon the web on February 25, 1995, with four pathways; it is now starting its 12th year, with 150 pathways. Happy birthday, UM-BBD! Students in our 2006 Biocatalysis and Biodegradation class, offered completely over the Internet, have examined websites on the UM-BBD Useful Internet Resources page and selected the most interesting ones. The Useful Internet Resources page now links to the list of these choices and the reason each site was selected. On the Useful Internet Resources page, a link was added for the Chemical Suppliers Directory.

January 18, 2006
One new reaction mechanism graphic has been added, for the styrene monooxygenase reaction in the Styrene pathway. This brings the number of such graphics to 34. A list of all reaction mechanism graphics is available. A new publication is available: Ellis, L.B.M., Roe, D., and Wackett, L.P. (2006) "The University of Minnesota Biocatalysis/ Biodegradation Database: The First Decade" Nucleic Acids Research 34: D517-D521. The full text of this paper is linked to on the UM-BBD home page and publication page. Cite the database using this paper or its successors. The What's New page restarts; 2005 activities have been archived.

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