Journal of Computational Chemistry
Design patterns: elements of reusable object-oriented software
Design patterns: elements of reusable object-oriented software
Approximate decision algorithms for point set congruence
Computational Geometry: Theory and Applications
Object-oriented software construction (2nd ed.)
Object-oriented software construction (2nd ed.)
New contact measures for the protein docking problem
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Model-Based Object Recognition by Geometric Hashing
ECCV '90 Proceedings of the First European Conference on Computer Vision
A novel three-dimensional collaborative online platform for bio-molecular modeling
SG'10 Proceedings of the 10th international conference on Smart graphics
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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 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 inMolecular 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, extensibility, and robustness 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.