3 research outputs found
Lattice model refinement of protein structures
To find the best lattice model representation of a given full atom protein
structure is a hard computational problem. Several greedy methods have been
suggested where results are usually biased and leave room for improvement. In
this paper we formulate and implement a Constraint Programming method to refine
such lattice structure models. We show that the approach is able to provide
better quality solutions. The prototype is implemented in COLA and is based on
limited discrepancy search. Finally, some promising extensions based on local
search are discussed.Comment: In Proceedings of Workshop on Constraint Based Methods for
Bioinformatics (WCB 2010); Jul 21, 2010; Edinburgh, UK (co-located with ICLP
2010); 7 page
Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains
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.Comment: Published in Proceedings of the Fifth Workshop on Constraint Based
Methods for Bioinformatics (WCB09), 2009, 10 page
A Hybrid Local Search for Simplified Protein Structure Prediction
Protein structure prediction based on Hydrophobic-Polar energy model
essentially becomes searching for a conformation having a compact hydrophobic
core at the center. The hydrophobic core minimizes the interaction energy
between the amino acids of the given protein. Local search algorithms can
quickly find very good conformations by moving repeatedly from the current
solution to its "best" neighbor. However, once such a compact hydrophobic core
is found, the search stagnates and spends enormous effort in quest of an
alternative core. In this paper, we attempt to restructure segments of a
conformation with such compact core. We select one large segment or a number of
small segments and apply exhaustive local search. We also apply a mix of
heuristics so that one heuristic can help escape local minima of another. We
evaluated our algorithm by using Face Centered Cubic (FCC) Lattice on a set of
standard benchmark proteins and obtain significantly better results than that
of the state-of-the-art methods