BMC Bioinformatics
Volume 9
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Abstract (provisional)
Background
The principles of protein folding and evolution pose
problems of very high inherent complexity.
Often these problems are tackled using simplified protein models,
e.g. lattice proteins.
The CPSP-tools package provides programs to solve exactly and completely
the problems typical of studies using 3D lattice protein models.
Among the tasks addressed are the prediction of (all) globally optimal
and/or suboptimal structures as well as sequence design and neutral
network exploration.
Results
In contrast to stochastic approaches, which are
not capable of answering many fundamental questions, our methods
are based on fast, non-heuristic techniques.
The resulting tools are designed for high-throughput studies of
3D-lattice proteins utilising the Hydrophobic-Polar (HP) model.
The source bundle is freely available at
http://www.bioinf.uni-freiburg.de/sw/cpsp/
Conclusions
The CPSP-tools package is the first set
of exact and complete methods for
extensive, high-throughput studies of non-restricted 3D-lattice
protein models. In particular, our package deals with cubic and
face centered cubic (FCC) lattices.
The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.
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