Biomedical Engineering Reference
In-Depth Information
methane, lists associated identifi ers including carbon, diamond, soot, fullerene,
and many other more complex organic molecules. There are multiple hits for
well - defi ned compounds such as vancomycin and taxol and other much more
simple organic molecules. While useful, PubChem is, quite simply, inappropri-
ate to treat as an authority.
5.4.2
Other Molecule Databases
Another interesting database of relevance to biomedical researchers is the
Chemical Entities of Biological Interest, or ChEBI database (http://www.
ebi.ac.uk/chebi/). The data are curated on an ongoing basis and as of this
writing ChEBI release 69 is available, with 584,456 total entities, of which
21,369 are fully annotated and curated. ChEBI includes an ontology which
identifi es the relationships between molecular entities or classes of entities
and their “ parents ” and/or “ children ” . Another database of primary interest
to biomedical researchers is DrugBank (http://www.drugbank.ca/), a manually
curated database [20] linking out to other public domain databases [e.g., the
Kyoto Encyclopedia of Genes and Genomes, KEGG, (http://www.genome.jp/
kegg/) [21], PubChem, ChEBI, the protein databank (PDB, http://www.pdb.org/
pdb/home/home.do ), Swiss - Prot ( http://www.expasy.ch/sprot/ ), and GenBank
(http://www.ncbi.nlm.nih.gov/genbank/)] and additional data from the labora-
tories of the hosts. The database aggregates both bioinformatics, cheminfor-
matics data, detailed drug data, and comprehensive drug target information
and contains U.S. Food and Drug Administration (FDA)-approved small-
molecule and biotech drugs representing nearly 5000 molecules [22]. For those
interested in vendor libraries for use for docking studies, ZINC (http://
zinc.docking.org/index.shtml) represents a free, searchable database of over
20 million molecules commercially available compounds for virtual screening
available as three-dimensional structures [23, 24]. Importantly all the mole-
cules are assigned biologically relevant protonation states and are annotated
with other molecular properties which may be of interest for hit fi ltering.
5.4.3
ChemSpider
Another example of a freely available database (also described in Chapter 22)
is ChemSpider (http://www.chemspider.com/) [15, 16], a community resource
for chemists provided by the Royal Society of Chemistry. It currently contains
almost 25 million unique chemical entities aggregated from almost 400 diverse
data sources, including government databases, chemical vendors, commercial
database vendors, publishers, as well as all of the prior described databases
and individual chemists. The unique capabilities of ChemSpider relative to
other public chemistry databases include the real-time curation of the data by
the community and annotation of the data. It is also possible to deposit New
data to the database: New chemical compounds can be deposited to the data-
base as singletons or as large collections with up to half a million compounds
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