Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains
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The simulation of a protein's folding process is often done via stochastic local search, which requires a procedure to apply structural changes onto a given conformation. Here, we introduce a constraint-based approach to enumerate lattice protein structures according to k-local moves in arbitrary lattices. Our declarative description is much more flexible for extensions than standard operational formulations. It enables a generic calculation of k-local neighbors in backbone-only and side chain models. We exemplify the procedure using a simple hierarchical folding scheme.
Published in Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009, 10 pages
Published in Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009, 10 pages
Keywords
Computational Engineering, Finance, and Science, Biomolecules, D.1.6; G.2.1; J.2; J.3