Metabolic Pathway Databases & Related
Bioinformatics & Genomics
Companies, Publishers, & Books
Compendiums & Lists of Resource Links
Compounds & Enzymes
Educational & Information Resources
Genomics & DNA Sequence Analysis
Hidden Markov Models
Major Sites & Organizations
Metabolic Pathway Databases & Related
Molecular Modeling & Visualization
Motif, Domain, Profile, Pattern, & Repeat Searches
Multiple Alignment & Phylogeny
Protein & Nucleic Acid Search Servers
Protein Analysis from Sequence
Sites with Multiple or Integrated Tools
Software Catalogues, Lists, & Downloads
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[University of Minnesota] “Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds.”
[ExPASy] A searchable index of biochemical pathways.
[SRI International] The BioCyc Knowledge Library is the new name for EcoCyc and MetaCyc. It is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from many organisms.
Biomolecular Interaction Network
The page describes BIND, which will span the complexity of interaction information gathered through experimental studies of biomolecular interactions. BIND contains interaction, molecular complex, and pathway records.
Cell Signaling Networks Database
[National Institute of Health Sciences, Japan] CSNDB “is a data- and knowledge- base for signaling pathways of human cells. It compiles the information on biological molecules, sequences, structures, functions, and biological reactions which transfer the cellular signals.”
[Argonne National Laboratories] The EMP database contains detailed information on a very large number of enzymes from over 17,000 articles. It can be searched by name, EC number, taxon, tissue, or organelle.
Kyoto Encyclopedia of Genes and Genomes
[GenomeNet] “KEGG is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene
catalogs produced by genome sequencing projects.”
Links to Pathway and Other Databases
[GenomeNet] A comprehensive list of links to biological and biochemical databases. The types of databases include: metabolic pathways; enzymes, compounds, and elements; regulatory pathways; protein-protein interactions; nomenclature and classification; taxonomy; and complete genomes and analysis.
Links to Pathway Databases
[Kyoto University] A list of links to databases of pathways of reactions & compounds in living cells.
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[Yale University] The metabolic component of SoyBase, a soybean genetic database, contains reaction and pathway descriptions and diagrams for a number of basic metabolic pathways.
Metabolic Pathways of Biochemistry
[Karl J. Miller] (George Washington University) This site is designed to graphically represent all major metabolic pathways, primarily those important to human biochemistry.
Metabolism & Biocompounds Resources
[University of Nebraska, Lincoln] Links to metabolism, metabolic pathway and biocompound databases and information resources.
Ortholog/Paralog Groups of Functional Units
[Institute for Chemical Research, Kyoto University] Conserved gene clusters in the KEGG metabolic and regulatory pathways.
[NCGR] PathDB is a database of biochemical pathways and metabolism, and is able to store rich information about pathways, enzymes, reactions, transport steps, and biochemical compounds.
[Cornell and Iowa State University] This database contains genomic and metabolic information for soybeans.
SPAD: Signaling PAthway Database
[Kyushu University] An integrated database for genetic information and signal transduction systems.
stke: Signal Transduction Knowledge Environment
[Science journal, Stanford University library] Web resource for biological (cellular) signal transduction, emphasizing articles, news, meetings, and links.