ayout 1 - EMBL Grenoble

EMBL Research at a Glance 2009
Christoph
Steinbeck
PhD 1995, Rheinische
Friedrich-Wilhelm-Universität,
Bonn.
Postdoctoral research at
Tufts University, Boston and
the Max-Planck-Institute of
Chemical Ecology, Jena,
Germany, 1997-2002.
Habilitation, 2003, Organic
Chemistry, Friedrich-Schiller-
Universität, Jena, Germany,
2003.
Head of Research Group for
Molecular Informatics,
Cologne University
Bioinformatics Center
(CUBIC), 2002-2007.
Lecturer in
Chemoinformatics, University
of Tübingen, 2007.
Team leader at EMBL-EBI
since 2008.
Chemoinformatics and metabolism
Previous and current research
The Chemoinformatics and Metabolism team aims to provide the biomedical community with
information on small molecules and their interplay with biological systems. The group develops
methods to decipher, organise and publish the small molecule metabolic content of organisms. We
develop tools to quickly determine the structure of metabolites by stochastic screening of large candidate
spaces and enable the identification of molecules with desired properties. This requires algorithms
for the prediction of spectroscopic and other physicochemical properties of chemical
graphs based on machine learning and other statistical methods.
We are further investigating the extraction of chemical knowledge from the printed literature by
text and graph mining methods, improved dissemination of information in life science publications,
as well as open chemoinformatics workflow systems. Together with an international group
of collaborators we develop the Chemistry Development Kit (CDK), the leading open source library
for structural chemoinformatics as well as the chemoinformatics subsystem of Bioclipse, an
award-winning rich client for chemo- and bioinformatics.
Future projects and goals
ChEBI datasets to aid the human curators. Last but not least, 2009
will reveal the EBI’s solution on how to integrate the chemogenomic
data with existing chemical resources at the institute.
The recently acquired resource of large-scale drug activity data at the EBI creates exciting new opportunities
both on the research and service side (www.ebi.ac.uk/Information/News/
pdf/Press23July08.pdf). Our team has started to create an open source chemical search engine for
the new resource, which will be the first open source chemistry search engine for the widely used
OracleTM Database system. A combination of the new chemogenomics data and the Chemistry
Development Kit will allow us to create open structure-activity models and to assist efforts in wet
lab screening in areas such as library design.
On the service side, ensuring a sustainable growth for the ChEBI database will be the focus of our
attention. The number of marketed and developed drugs in the world drug index alone currently
amounts to more than 80,000 compounds. Assuming only a handful of metabolites are produced
by organisms upon application of these drugs, the task ahead takes shape. Not only does this task
require a larger team for data collection and curation but also research into the automated assembly
and validation of
Computer-Assisted Structure Elucidation uses a structure generation
engine to produce chemical spaces based on boundary conditions such
as the gross formula of the unknown compound, determined for instance
by mass spectrometry. These chemical spaces are then crawled and
candidate structures in them inspected for fitness by comparing predicted
and measured properties such as NMR spectra. Based on calculated
fitness values, a ranking is presented to the user.
Selected references
Kuhn, S. et al. (2008). Building blocks for automated elucidation of
metabolites: Machine learning methods for NMR prediction. BMC
Bioinformatics, 9, 00
Willighagen, E.L. et al. (2007). Userscripts for the life sciences. BMC
Bioinformatics, 8, 87
Han, Y.Q. & Steinbeck, C. (200). Evolutionary-algorithm-based
strategy for computer-assisted structure elucidation. J. Chem. Inf.
Com. Sci., , 89-98
Steinbeck, C. (2001). SENECA: A platform-independent, distributed,
and parallel system for computer-assisted structure elucidation in
organic chemistry. J. Chem. Inf. Com. Sci., 1, 1500-1507
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