Web Resources
Metabolic Pathways Databases
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The Biomolecular Interaction
Network Database (BIND): A collection of records documenting molecular interactions. Interactions
are the basic units of BIND and can be linked together to form molecular complexes or pathways.
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MetaCyc: A metabolic
pathway database that stores experimentally elucidated metabolic pathways from more than 300 different
organisms. It describes metabolic pathways, reactions, enzymes, and substrate and product compounds.
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Reactome: A database
of biological pathways and processes. Reactome is an effort to develop a curated resource of core
pathways and reactions in human biology. The information in the Reactome database database is authored
by biological researchers, maintained by the Reactome editorial staff, and cross-referenced with
PubMed,
GO, and the
sequence databases at NCBI,
Ensembl, and
UniProt. Reactome is
a free on-line resource, and the Reactome software is open-source.
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Enzymes and Metabolic Pathways
Database (EMP): EMP is an online tool for searching and analyzing enzyme and metabolic pathway data.
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Blueprint:
Blueprint has tools for actively researching protein folding and molecular structure, location, dynamics,
sequence, interaction and evolution as they relate to systems biology. These are part of the effort
towards simulating a living cell.
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Kyoto Encyclopedia of Genes
and Genomes (KEGG): KEGG is developed to be a complete computer representation of the cell and the
organism. This will enable computational prediction of higher-level complexity of cellular processes and
organism behaviors from genomic information. KEGG consists of a set of databases and software to utilize
these databases, including a pathway database, gene databases and compound-reaction databases.
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Pathway Analysis Tools for
Integration and Knowledge Acquisition (PATIKA): PATIKA is a project for the development of tools for
effective integration, querying, analysis, and manipulation of pathway data.
Protein Databases
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Protein Information
Resource (PIR): PIR has a protein sequence database of fuctionally annotated protein sequences. It also
has a protein family classification system, a protein classification database, and a non-redundant
reference protein database.
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Swiss-Prot:
The SwissProt protein database is a curated and annotated protein sequence database with facilities for
integration with other databases.
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Protein Data Bank (PDB):
PDB consists of a database and the tools to process three-dimensional macromolecular structure data.
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TrEMBL: TrEMBL is
an annotated protein sequence database that contains the translation of coding sequences in the
EMBL,
GenBank, and
DDBJ nucleotide
sequence databases.
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The Database of
Interacting Proteins (DIP): DIP serves as a database of experimentally determined interactions
between proteins. It combines information from a variety of sources to create a single, consistent set
of protein-protein interactions. The data stored within the DIP database are curated, both manually by
expert curators and also automatically using computational approaches.
Gene Databases
