CPSP-tools--exact and complete algorithms for high-throughput 3D lattice protein studies.
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 1.


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.
Mann
Martin
M
Bioinformatics Group, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany. mmann@informatik.uni-freiburg.de
Will
Sebastian
S
Backofen
Rolf
R
D000465:Algorithms; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D011506:Proteins