MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a collaborative project between the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute. MACiE currently contains 213 fully annotated enzyme reaction mechanisms, which comprise 209 EC numbers (160 EC sub-subclasses) and 308 distinct CATH codes.

sMOL Explorer is a 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction, and statistical analysis and data mining through Web interface. With sMOL Explorer, users can create his/her own database by adding each small molecule via a drawing interface or uploading the data files from internal and external projects into the sMOL database. Then, the database can be browsed and queried with textual and structural similarity search. The molecule can also be submitted to search against external public databases including PubChem, KEGG, DrugBank and eMolecules. Moreover, users can easily access a variety of data mining tools to perform analysis including (1) finding the frequent substructure, (2) clustering the molecular fingerprints, (3) identifying and removing irrelevant attributes from the data, and (4) building the classification model of biological activity.

The Human Metabolome Library (HML) is a one-stop chemical resource to order/acquire one or more compounds to confirm, validate or quantify suspected metabolites in tissues or biofluids. The Human Metabolome Library has been developed through the efforts of the Human Metabolome Project. Users may order or request any reasonable quantity (1 mg – 100 g) for as many as 100 compounds at a time. Currently the HML has 818 compounds listed on the HML website, including purchased, synthesized and purified compounds. Through this HML website collaborators and commercial labs are able to request compounds through the HML’s electronic order forms. Researchers may obtain metabolites from the HML in one of two ways. Scientists wishing to use these compounds for basic research purposes or in collaborative efforts with the HML are given access to the compounds as long as they acknowledge the Human Metabolome Project (and Genome Alberta) through co-authorship or acknowledgements. To our collaborators, we ask that you charge only shipping/ handling fees.

BDPServer predicts whether chemical compounds can be biodegraded or not. Chemical compound descriptions can be typed directly in SMILES format or drawn with the JME applet. Solubility information is optional. The JME applet has been provided by Peter Ertl, from Novartis.

Metabolomics of Starvation Home Metabolomics of Starvation Homepage Authors and contributors to the Metabolomics of Starvation project Figures and Tables from the publication Supplemental figures and tables Download data used in the publication Links to relevant sites Home Conservation of the metabolomic response to starvation across divergent microbes Matthew J. Brauer Jie Yuan Bryson Bennett Wenyun Lu Elizabeth Kimball David Botstein Joshua Rabinowitz [ Home | Authors | Figures and Tables | Supplemental | Download | Links ]

PRIMe, Platform for RIKEN Metabolomics, is a web-based service for metabolomics and transcriptomics as systems understanding of life science. This project performs standard-metabolites measurements by multi-dimensional NMR spectroscopy, GC/MS, LC/MS and CE/MS. We also provide unique tools which are useful for metabolomics, transcriptomics and integrated analysis of different omics data.

BioMeta is a database of metabolites and metabolic reactions. Its contents are largely based on the KEGG Ligand database. Compared to the KEGG database, a large number of chemical structures have been corrected with respect to constitution and stereochemistry. Our aim is to arrive at a database with correct representations of molecules and reactions. About 1,500 molecular structures have been corrected and about 55% of the unbalanced reactions have been "balanced". Currently, the contents of the BioMeta database are based on version 36 of the KEGG Ligand database (October 25, 2005) but an update is underway. The interface to the database is meant to be intuitive, but extensive help pages are also provided.

Our research focuses on the development and application of liquid chromatography-mass spectrometry based (LC-MS) global metabolite profiling as a general discovery tool in chemical biology.