Masahiro Hattori

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A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to(More)
KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to(More)
The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for(More)
LIGAND is a composite database comprising three sections: COMPOUND for the information about metabolites and other chemical compounds, REACTION for the collection of substrate-product relations representing metabolic and other reactions, and ENZYME for the information about enzyme molecules. The current release (as of September 7, 2001) includes 7298(More)
Cellular functions result from intricate networks of molecular interactions, which involve not only proteins and nucleic acids but also small chemical compounds. Here we present an efficient algorithm for comparing two chemical structures of compounds, where the chemical structure is treated as a graph consisting of atoms as nodes and covalent bonds as(More)
The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPred(More)
We have developed an efficient algorithm for comparing two chemical compounds, where the chemical structure is treated as a 2D graph consisting of atoms as vertices and covalent bonds as edges. Based on the concept of functional groups in chemistry, 68 atom types (vertex types) are defined for carbon, nitrogen, oxygen, and other atomic species with(More)
The SNARE proteins are required for membrane fusion during intracellular vesicular transport and for its specificity. Only the unique combination of SNARE proteins (cognates) can be bound and can lead to membrane fusion, although the characteristics of the possible specificity of the binding combinations encoded in the SNARE sequences have not yet been(More)
The EC (Enzyme Commission) numbers represent a hierarchical classification of enzymatic reactions, but they are also commonly utilized as identifiers of enzymes or enzyme genes in the analysis of complete genomes. This duality of the EC numbers makes it possible to link the genomic repertoire of enzyme genes to the chemical repertoire of metabolic pathways,(More)
MOTIVATION The IUBMB's Enzyme Nomenclature system, commonly known as the Enzyme Commission (EC) numbers, plays key roles in classifying enzymatic reactions and in linking the enzyme genes or proteins to reactions in metabolic pathways. There are numerous reactions known to be present in various pathways but without any official EC numbers, most of which(More)