Structure Optimization by an Improved Tabu Search in the AB Off-Lattice Protein Model

Abstract

Tabu search is a meta-heuristic approach that is found to be useful in solving combinatorial optimization problems. This paper employs the adaptive memory features of tabu search to deal with protein folding problem. A kind of optimization of the neighborhood scale is presented, where a annealing mechanism is also used to enhance the searching ability for optimum solutions of the AB off-lattice model. This model has only two types of residues: hydrophobic (A) and hydrophilic(B). Based on the AB off-lattice model, the problem is converted from a nonlinear constraint-satisfied problem to an unconstrained optimization problem. Experimental results demonstrate that the proposed methods are very promising for searching the ground states of protein folding in two dimensions.