Ellis, L.B., Hershberger, C.D., and Wackett, L.P.. "The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics." Nucleic Acids Res. 27
(1).
1999.
pp. 373-6.
[ .pdf ] [ PubMed ]
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://www.labmed.umn.edu/umbbd/i nde x.html) first became available on the web in 1995 to provide information on microbial biocatalytic reactions of, and biodegradation pathways for, organic chemical compounds, especially those produced by man. Its goal is to become a representative database of biodegradation, spanning the diversity of known microbial metabolic routes, organic functional groups, and environmental conditions under which biodegradation occurs. The database can be used to enhance understanding of basic biochemistry, biocatalysis leading to speciality chemical manufacture, and biodegradation of environmental pollutants. It is also a resource for functional genomics, since it contains information on enzymes and genes involved in specialized metabolism not found in intermediary metabolism databases, and thus can assist in assigning functions to genes homologous to such less common genes. With information on >400 reactions and compounds, it is poised to become a resource for prediction of microbial biodegradation pathways for compounds it does not contain, a process complementary to predicting the functions of new classes of microbial genes.
Keywords: Bacteria_genetics ; Bacteria_*metabolism ; Bacterial Proteins_metabolism ; *Biodegradation ; Biotechnology ; *Catalysis ; *Databases Factual_trends ; Environmental Pollution ; Enzymes_chemistry ; Enzymes_genetics ; Enzymes_metabolism ; Genes ; Bacterial_genetics ; Genes ; Bacterial_physiology ; Human ; Information Storage and Retrieval ; Internet ; Minnesota ; Universities
Karp, P.D., Riley, M., Paley, S.M., and Pellegrini-Toole, A.. "The MetaCyc Database." Nucleic Acids Res. 30
(1).
2002.
pp. 59-61.
[ .pdf ] [ PubMed ]
MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms. MetaCyc is a review-level database in that a given entry in MetaCyc often integrates information from multiple literature sources. The pathways in MetaCyc were determined experimentally and are labeled with the species in which they are known to occur based on literature references examined to date. MetaCyc contains extensive commentary and literature citations. Applications of MetaCyc include pathway analysis of genomes, metabolic engineering and biochemistry education. MetaCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. MetaCyc is available via the World Wide Web at http://ecocyc.org/ecocyc/metacyc.html, and is available for local installation as a binary program for the PC and the Sun workstation, and as a set of flatfiles. Contact metacyc-info
Keywords: Comparative Study ; Database Management Systems ; *Databases Protein ; Enzymes_chemistry ; Enzymes_*metabolism ; Genome ; Human ; Information Storage and Retrieval ; Internet ; *Metabolism
Zauner, K.P. and Conrad, M.. "Enzymatic computing." Biotechnol Prog. 17
(3).
2001.
pp. 553-9.
[ .pdf ] [ PubMed ]
The conformational dynamics of enzymes is a computational resource that fuses milieu signals in a nonlinear fashion. Response surface methodology can be used to elicit computational functionality from enzyme dynamics. We constructed a tabletop prototype to implement enzymatic signal processing in a device context and employed it in conjunction with malate dehydrogenase to perform the linearly inseparable exclusive-or operation. This shows that proteins can execute signal processing operations that are more complex than those performed by individual threshold elements. We view the experiments reported, though restricted to the two-variable case, as a stepping stone to computational networks that utilize the precise reproducibility of proteins, and the concomitant reproducibility of their nonlinear dynamics, to implement complex pattern transformations.
Keywords: Calcium_chemistry ; Calcium_metabolism ; Enzymes_*chemistry ; Enzymes_*metabolism ; Image Processing ; Computer-Assisted ; Magnesium_chemistry ; Magnesium_metabolism ; Malate Dehydrogenase_chemistry ; Malate Dehydrogenase_metabolism ; Models Chemical ; *Models Molecular ; Osmolar Concentration ; Protein Conformation