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Animal Toxin Database

Description :
Database of animal toxins


Description :
Bacteriocin natural antimicrobial peptides


Description :
Database of commercially-available compounds for virtual screening and chemoinformatics


Description :
RESP and ESP atomic charges and force field libraries for small molecules and molecular fragments


Description :
Database of flavors and scents


Description :
A comprehensive database of toxic compounds

Glycoconjugate Data Bank

Description :
Annotated structures of glycan molecules


Description :
The most commonly employed analytical tools used in high-throughput metabolic profiling, known as metabolomics or metabonomics, are nuclear magnetic resonance (NMR) and mass spectrometry (MS). However, bioinformatics resources for identifying common metabolites from experimental NMR and MS data have been limited. The Madison Metabolomics Consortium Database (MMCD) is a web-based tool that contains data pertaining to biologically-relevant small molecules from a variety of species. The MMCD contains information on 20,306 metabolites and other small molecules of biological interest. These molecules, which were chosen from entries in KEGG, BioCyc, CHEBI, HMDB, UM-BBD, and PDB, represent a collection of primary and secondary metabolites, xenobiotics, and common small molecule contaminants. A total of 477 small molecule entries contain experimental NMR data from the growing BMRB collection. The MMCD is equipped with a flexible and efficient query system that supports complex queries from any combination of its five basic search engines: text, structure, NMR, mass, and miscellanea. Results returned give users access to all of the MMCD information about a molecule and offer direct links to records in other public databases.

References :
Cui, Q., Lewis, I.A., Hegeman, A.D., Anderson, M.E., Li, J., Schulte, C.F., Westler, W.M., Eghbalnia, H.R., Sussman, M.R., and Markley, J.L. (2008) Metabolite identification via the Madison Metabolomics Consortium Database. Nature Biotechnology, 26, 162

Comparative Toxicogenomics Database

Description :
A knowledgebase for curated chemical-gene-disease networks


Description :
eMolecules is a search engine for chemical structures that allows for substructure searching.


Description :
PubChem contains the chemical structures of small organic molecules and information on their biological activities. PubChem can be searched by keywords, chemical properties, and structural similarity. PubChem s chemical structure records are linked to other NCBI databases including PubMed.


Description :
Target Fishing Dock (TarFisDock) is a web server that docks small molecules with protein structures in the Potential Drug Target Database (PDTD) in an effort to discover new drug targets.


Description :
Superimpose web server performs structural similarity searches for small molecules, parts of proteins (i.e. binding sites) or whole proteins, with a preference towards 3D structure based methods. Users are assisted in selection of algorithms and databases that best suit their needs.


Description :
PharmaGist is a web server for detecting pharmacophores or the spatial arrangement of features that enables a molecule to interact with a specific target receptor. Users input a set of structures of molecules that bind with the receptor for outputs of candidate pharmacophores that can be used in rational drug design.


Description :
ChemBank is a public, web-based informatics environment created by the Broad Institute s Chemical Biology Program and funded in large part by the National Cancer Institute s Initiative for Chemical Genetics (ICG). This knowledge environment includes freely available data derived from small molecules and small-molecule screens, and resources for studying the data such that biological and medical insights can be gained from their results. ChemBank is intended to guide chemists synthesizing novel compounds or libraries, to assist biologists searching for small molecules that perturb specific biological processes, and to catalyze the process by which new and effective medicines are discovered.

ChemBank stores an increasingly varied set of cell measurements derived from various biological objects, including cell lines treated with small molecules. Analysis tools are available and are being developed that allow the relationships between cell states, cell measurements, and small molecules to be determined. Small molecules contained with ChemBank are manually annotated with biological activities from the primary literature using both internal and publicly available controlled vocabularies such as Medical Subject Headings (MeSH) and the Gene Ontology (GO). Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the ICG in collaborations involving biomedical researchers worldwide. These scientists have agreed to perform their experiments in an open data-sharing environment.

The primary goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available almost exclusively in the private sector. ChemBank is intended to be a planning and discovery tool for chemists and biologists, as well as those interested in finding new therapeutic drugs. In sum, ChemBank is an evolving knowledge environment that can be freely used to extract knowledge from public experiments whose greatest value is likely to reside in their collective sum.

Recent develoments :
For recent developments in ChemBank, please see the Release Notes (

Aknowledgement :
ChemBank has been funded in large part with federal funds from the National Cancer Institute’s Initiative for Chemical Genetics, National Institutes of Health, under Contract No. N01-CO-12400. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the U.S. Government. Additional funding has been received from the National Institute of General Medical Sciences, the NIH RoadMap Network of Exploratory Centers for Cheminformatics Research and the National Institute of Diabetes and Digestive and Kidney Diseases.

References :
1. Tolliday N, Clemons PA, Ferraiolo P, Koehler AN, Lewis TA, Li X, Schreiber SL, Gerhard DS, Eliasof S. (2006) Small molecules, big players: the National Cancer Institute s Initiative for Chemical Genetics. Cancer Res. 66,8935-8942.