Biology Reference
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DATABASES AND SUPPORTING TOOLS FOR IN SILICO MODELING
AND SIMULATION
Integrated Metabolic Database System
Recent years have seen an explosion in the amount of biological data
and information. This has resulted in the development of various data-
bases containing biological information at different levels ranging from
DNA sequences to metabolic pathways [71]. Among them, metabolic
databases provide all available information on metabolic pathways,
reactions, and enzymes that are essential to the elucidation of the
metabolic and physiological characteristics of organisms. Currently
available public metabolic databases are given in table 7.1. These data-
bases, however, possess different data collections, which will become
much more usable if they are unified into composite resources with
common interfaces [72-74]. To properly handle such redundant and
heterogeneous data sources scattered over different sites, an integrated
metabolic database system, BioSilico, was developed [75]. BioSilico
integrates publicly available metabolic databases for efficient navigation
and analysis of metabolic pathway information.
B
IO
S
ILICO
BioSilico is a comprehensive, web-based database system that facilitates
the search and analysis of metabolic pathways. Inhomogeneous meta-
bolic databases including LIGAND, ENZYME, EcoCyc, and MetaCyc
are compiled and integrated in a systematic way, thereby allowing
users to efficiently retrieve and explore the relevant information on
Table 7.1 Representative metabolic databases useful for studying enzymes,
metabolites, reactions, and pathways
Database
Corresponding URL
Biocarta
BioCyc
BioSilico
BRENDA
EcoCyc
ENZYME
ERGO-LIGHT
KEGG
Klotho
LIGAND
MetaCyc
PathDB
UMBBD
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