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sis capabilities could help to boost the use of Scaffold
Hunter. The development and integration of addi-
tional functionality is encouraged by a modular soft-
ware architecture designed to be easily extendable
and by providing the software as open source.
A promising direction to enhance the currently
supported classification concepts based on tree-like
hierarchies is to support network-like structures. Re-
cently an extension of the scaffold tree approach was
proposed taking all possible parent scaffolds into ac-
count (Varin et al., 2011). This creates so-called scaf-
fold networks, which were shown to reveal additional
scaffolds having a desired biological property. Fur-
thermore networks can be used to represent struc-
tural similarities, e.g. derived from maximum com-
mon substructures, and might prove to be more flexi-
ble when ring-free molecules are considered or func-
tional side-chains should be taken into account. How-
ever, visualizing networks instead of tree-like hierar-
chies without compromising the orientation is chal-
lenging. New navigation concepts have to be devel-
oped and graph layout techniques must be customized
to the specific characteristics of such networks. We
plan to make use of the Open Graph Drawing Frame-
work (OGDF, 2011) for that purpose.
Due to the dynamic nature and the growing extent
of publicly available chemical data it might be help-
ful to also allow direct access to public resources from
within the GUI, e.g., by providing direct links to Pub-
Chem web pages for database compounds.
Scaffold Hunter is implemented in Java and freely
available under the terms of the GNU GPL v3 at
http://scaffoldhunter.sourceforge.net/.
ACKNOWLEDGEMENTS
We would like to thank the participants of student
project group PG552, the group of Prof. Waldmann,
in particular Claude Ostermann and Bj
¨
orn Over, Ste-
fan Mundt, Stefan Wetzel, and Steffen Renner for
their valuable suggestions and their contributions to
the project.
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