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KEGG PEPTIDE : A Database for Peptide Structures

Genomic information provides a wealth of knowledge to extract the design principles of the biological system. Most of the post-genomic researches focus on describing how the components of the biological system assemble into complex networks to execute autonomous functions on the basis of genome, transcriptome and proteome analyses. Chemical compounds such as metabolites, hormones and drugs are also parts of the major components in the biological system, such that it is of great importance to investigate the correlation between genomic and chemical information in a systematic manner. A lot of information on the chemical genomics has been so far accumulated in extensive literature and databases with respect to biosynthetic pathways, metabolic pathways and drug targets [1-4]. In order to extract significant knowledge lying under the chemical genomic information from the data scattered across different sources, it is necessary to perform an integrated analysis of genomic information (genes and proteins) and chemical information (chemical substances and their reactions). Peptide information provides a suitable opportunity for the integrated analysis since peptide is one of the chemical compounds highly correlated with genomic information. The diverse functions of peptides extend from antimicrobial activities to the control of biological functions, thereby antimicrobial peptide databases, such as APD [5] and ANTIMIC [6], are constructed to collect peptide information from functional aspects. On the other hand, most peptides are gene encoded to be produced through maturing process (ribosomal peptide), while others are enzymically synthesized as secondary metabolites (nonribosomal peptide). The chemical genomic information in the biosynthetic process besides the functional information includes a lot of knowledge to understand the design principles in the production of peptides coded on genomic information. We thus expand the KEGG LIGAND database to include PEPTIDE for the integrated analysis of peptide and genomic information from the chemical genomic viewpoints.