Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains
Computational Engineering, Finance, and Science
2009-10-21 v1 Biomolecules
Abstract
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.
Keywords
Cite
@article{arxiv.0910.3880,
title = {Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains},
author = {Martin Mann and Mohamed Abou Hamra and Kathleen Steinhöfel and Rolf Backofen},
journal= {arXiv preprint arXiv:0910.3880},
year = {2009}
}
Comments
Published in Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009, 10 pages