Databases

KEGG: Kyoto Encyclopedia of Genes and Genomes

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for linking genomes to life and the environment.

 

EcoCyc: Encyclopedia of Escherichia coli K-12 Genes and Metabolism

EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.

 

ExPASy Proteomics Server

Welcome to the ExPASy World Wide Web (WWW) proteomics server of the Swiss Institute of Bioinformatics (SIB). This server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.

 

BioCyc Home

BioCyc is a collection of 507 Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. 

 

Enzyme Database – BRENDA

BRENDA – The Comprehensive Enzyme Information System.

 

EzCatDB: A Database of Enzyme Catalytic Mechanisms

A Database of Enzyme Catalytic Mechanisms.

 

SABIO Reaction Kinetics Database (Version 20090423)

The SABIO-RK (System for the Analysis of Biochemical Pathways – Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.

 

BioNumbers – The Database of Useful Biological Numbers

The number you need, with references, in under a minute.

 

BioModels Database

BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.

SBML/Celldesigner format.

 

Reactome

Reactome – a curated knowledgebase of biological pathways

 

Orenza

Accurate and up to date list of Enzyme Activities for which no sequences are available in the main sequence protein databases.

 

BiGG Database

The BiGG database is a metabolic reconstruction of human metabolism designed for systems biology simulation and metabolic flux balance modeling. It is a comprehensive literature-based genome-scale metabolic reconstruction that accounts for the functions of 1,496 ORFs, 2,004 proteins, 2,766 metabolites, and 3,311 metabolic and transport reactions. It was assembled from build 35 of the human genome. Need an username and password.

 

ChemSpider

ChemSpider links together compound information across the web, providing free text and structure search access of millions of chemical structures.

 

HMDB

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found (and experimentally verified) in the human body. The database contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. HMDB contains information on more than 6500 metabolites. Additionally, approximately 1500 protein (and DNA) sequences are linked to these metabolite entries. Each MetaboCard entry contains more than 100 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets.