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Abstract:
In the next century, virtual laboratories will play a key role in
biotechnology. Computer experiments will not only replace
time-consuming and expensive real-world experiments, but they will also
provide insights that cannot be obtained using ``wet'' experiments.
The field that deals with the modeling of atoms, molecules, and their
reactions is called Molecular Modeling. The advent of
Life Sciences gave rise to numerous new developments in this
area. However, the implementation of new simulation tools is extremely
time-consuming. This is mainly due to the large amount of
supporting code ({\eg} for data import/export, visualization, and so on)
that is required in addition to the code necessary to implement the new idea. The
only way to reduce the development time is to reuse reliable code,
preferably using object-oriented approaches. We have designed and
implemented {\Ball}, the first object-oriented application framework for rapid
prototyping in Molecular Modeling. By the use
of the composite design pattern and polymorphism we were able to model
the multitude of complex biochemical concepts in a well-structured and
comprehensible class hierarchy, the {\Ball} kernel classes. The
isomorphism between the biochemical structures and the kernel classes
leads to an intuitive interface. Since {\Ball} was designed for rapid software
prototyping, ease of use and flexibility were our principal design
goals. Besides the kernel classes, {\Ball} provides fundamental
components for import/export of data in various file formats,
Molecular Mechanics simulations, three-dimensional visualization, and
more complex ones like a numerical solver for the Poisson-Boltzmann
equation. The usefulness of {\Ball} was shown by the
implementation of an algorithm that checks proteins for
similarity. Instead of the five months that an earlier implementation
took, we were able to implement it within a day using {\Ball}.
