Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A.. "The KEGG databases at GenomeNet." Nucleic Acids Res. 30
(1).
2002.
pp. 42-6.
[ .pdf ] [ PubMed ]
The Kyoto Encyclopedia of Genes and Genomes (KEGG) is the primary database resource of the Japanese GenomeNet service (http://www.genome.ad.jp/) for understanding higher order functional meanings and utilities of the cell or the organism from its genome information. KEGG consists of the PATHWAY database for the computerized knowledge on molecular interaction networks such as pathways and complexes, the GENES database for the information about genes and proteins generated by genome sequencing projects, and the LIGAND database for the information about chemical compounds and chemical reactions that are relevant to cellular processes. In addition to these three main databases, limited amounts of experimental data for microarray gene expression profiles and yeast two-hybrid systems are stored in the EXPRESSION and BRITE databases, respectively. Furthermore, a new database, named SSDB, is available for exploring the universe of all protein coding genes in the complete genomes and for identifying functional links and ortholog groups. The data objects in the KEGG databases are all represented as graphs and various computational methods are developed to detect graph features that can be related to biological functions. For example, the correlated clusters are graph similarities which can be used to predict a set of genes coding for a pathway or a complex, as summarized in the ortholog group tables, and the cliques in the SSDB graph are used to annotate genes. The KEGG databases are updated daily and made freely available (http://www.genome.ad.jp/kegg/).
Keywords: Computational Biology ; Computer Graphics ; *Databases Genetic ; *Databases Protein ; Gene Expression Profiling ; *Genome ; Human ; Information Storage and Retrieval ; Internet ; Macromolecular Systems ; Metabolism_genetics ; Multigene Family ; Protein Conformation ; Proteins_chemistry ; Proteins_genetics ; Proteins_metabolism ; Sequence Homology
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