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Cheminformatics
Free online resources
enabling crowd-sourced
drug discovery
The availability of freely accessible online resources to enable and support drug
discovery has blossomed in recent years. The PubChem platform is now
accompanied by a myriad of other online databases including ChEBI, DrugBank,
the Human Metabolome Database and ChemSpider. The access to the array of
software tools and diverse data in public domain provides capabilities
previously only available within the confines of organisations (eg, big Pharma)
that could afford significant investments in cheminformatics. This paper
provides an overview of the internet resources available to drug discovery
scientists and discusses the advantages of such accessibility but also the
potential risks that reside within the data. It also examines what the present
resources continue to lack and sets a vision for future approaches to providing
internet-based resources for drug discovery.
T
he past five years have seen a mini revolu- cific focus based on the domain expertise of the By Dr Antony J.
tion in the availability of resources to sup- hosting organisation; examples include databases Williams,
port drug discovery and, in particular, of curated literature data, chemical vendor cata- Valery Tkachenko,
databases searchable by molecular structure logues, patents, analytical data, biological data, Dr Chris Lipinski,
(Figure 1). Chemistry information on the internet etc. There are too many to include in this single Professor Alexander
continues to become more widely accessible and at article so only a small number will be discussed. Tropsha and
an increasing rate. There are many freely available For example, the authors recommend a recent arti- Dr Sean Ekins
chemical compound databases on the web
1,2
. cle that assesses the expanding public and com-
These databases generally contain the chemical mercial databases containing bioactive com-
identifiers in the form of chemical names (system- pounds
3
and conclude that the commercial efforts
atic and trade) and registry numbers. Since the files are ahead of the public ones.
in the databases are assembled in a heterogeneous The availability of molecule databases such as
manner, using variations in deposition processes PubChem (http://pubchem.ncbi.nlm.nih.gov/) has
and procedures to handle chemical structures, the dramatically changed the landscape of publicly
resulting data are plagued with inconsistencies and available cheminformatics resources, yet
quality issues. There are many databases available PubChem covers only a fraction of the chemical
from which the drug discovery community can universe, mostly of interest to chemical genomics
derive value. These databases generally have a spe- and pharmaceutical research. PubChem was
Drug Discovery World Winter 2009/10 33
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