Exact Methods for Simplified Protein Models

Monday, January 14, 2008 - 3:25pm - 3:40pm
EE/CS 3-180
Rolf Backofen (Albert-Ludwigs-Universität Freiburg)
Due to the inherent complexity of the associated problems,
investigations of the basic principles of protein folding and evolution
are usually restricted to simplified protein models.

Our group has developed methods and programs for exact and complete solving of
problems typical for studies using HP-like 3D lattice protein models.

Addressed tasks are the prediction of globally optimal and listing of
suboptimal structures, sequence design, neutral network exploration, and
degeneracy computation. The used methods are based on fast and
non-heuristic techniques (constraint programming) instead of following
stochastic approaches, which are not capable of answering many fundamental
questions. Thus, we are able to find optimal structure for HP-sequences of length
greater than 200, including a proof of optimality. We have used these methods to
find unique folding sequences, to investigate neutral nets and to design low-degenerated
sequences for given structures.
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