Biocatalysis databases

Biocatalysis http //dragon.labmed.umn.edu/ Iynda/index.html Biodegradation and Biocatalysis Database... 

Makes chemical structure drawings from ChemDraw and ISIS/Draw understandable to Microsoft Excel spreadsheets. Library of QSAR parameters for 250 substituents. Protecting Groups database with more than 20,000 reactions. Methods in Organic Synthesis (MOS) database with about 10,000 reactions, and the BioCatalysis database with biomolecule-mediated reactions. PCs, Macintosh, and Power Macintosh. 

University of Minnesota Biocatalysis/Biodegradation Database (umbbd.ahc.umn.edu) can be used to predict biodegradation pathways and biodegradation metabolites. Approximately two-thirds of the hazardous substances mentioned in the CERCLA Priority List of Hazardous Substances can be treated by different biotechnological methods. 

Table 5.5 Useful CD-ROM databases and Internet addresses to obtain biocatalysis information.

Gao, J., Ellis, L.B.M. and Wackett, L.P. (2010) The University of Minnesota Biocatalysis/Biodegradation Database improving public access. Nucleic Acids Res., 38, D488-D491. 

Biocatalysis/Biodegradation Database of the University of Minnesota Microbial metabolism of many chemicals http //www.labmed.umn.edu/umbbd/ index.html... 

Table 8.1 represents some of the enzymes (Jakoby and Ziegler, 1990) that participate in altering xenobiotics so as to make them either more readily excretable or less toxic for the storage. These enzymes have a preference for lipophilic compounds, although all hydrophilic compounds, are not excluded. Each enzyme has a phenomenally broad substrate range, and many appear to be inducible. The information for xenometabolism can be obtained from the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) at http //umbbd.ahc.umn.edu/ index.html (Ellis et al, 2000). 

Figure 8.3. Biocatalysis/biodegradation database for xenometabolism. The BBD is the primary resource for searching/retrieving information on xenobiotics and their metabolic pathways.

For biotechnological synthesis, there is a superb database containing information on miaobial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical componnds. It is called the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) at can be fonnd at http //nmbbd.ahc.umn.edu/search/index.html. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. 

The University of Minnesota has been adding to the Biocatalysis/Biodegradation Database [Ellis et al. 2003] since the early 1990s. It includes 144 pathways of microbial metabolism, mostly for xenobiotic degradation. 

Ellis, L. B. M B. K. Hou, W. Kang, and L. P. Wackett. 2003. The University of Minnesota Biocatalysis/Biodegradation Database Post-Genomic Datamining. Nucleic Acids Res 31 262-5. 

Ellis LBM, Wackett LP The University of Minnesota Biocatalysis/Biodegradation Database on the WWW http //dragon.labmed.iunn.edu/ lynda/index.html... 

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a data repository providing curated information on microbial catabolic enzymes and their organization into metabolic pathways 54. At present, the UM-BBD stores information on approximately 100 pathways with 700 reactions, 600 compounds and 400 enzymes. The database does not try to cover every known enzyme but rather focuses on those used for the biodegradation of xenobiotics. UM-BBD is linked to the ENZYME, BRENDA and KEGG/LIGAND databases mentioned above. 

The state of the art is described in many excellent and comprehensive books [4-29] and general review articles [30-70], The reference list gives only the most prominent and best known reviews. Additional and highly recommendable information sources for the synthetic chemist are the Warwick Biotransformation Abstracts and the associated electronic database. Contact address H.G. Crout, Warwick Biotransformation Club Database, Organic Chemical Institute, University of Warwick, UK (service for members only). The two CD-ROMs Biotransformation (K. Kieslich and the Warwick Biotransformation Club) and BioCatalysis (H.L. Holland and B. Jones) are available from Chapman Hall (London, 1996). Practical examples for preparative biotransformations (with checked procedures)... 

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