Protein Conformation of a Lattice Model Using Tabu Search

Authors:
P. M. Pardalos;Xin Liu;G. L. Xue
Affiliations:
Center for Applied Optimization, Department of Industrial and Systems Engineering, 303 Weil Hall, University of Florida, Gainesville, FL 32611. Email: {pardalos,liu}@ufl.edu;Center for Applied Optimization, Department of Industrial and Systems Engineering, 303 Weil Hall, University of Florida, Gainesville, FL 32611. Email: {pardalos,liu}@ufl.edu;Department of Computer Science and Electrical Engineering, College of Engineering and Mathematics, The University of Vermont, Burlington, VT 05405. Email: xue@cs.uvm.edu
Venue:
Journal of Global Optimization
Year:
1997

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Abstract

We apply tabu search techniques to the problem of determining the optimal configuration of a chain of protein sequences on a cubic lattice. The problem under study is difficult to solve because of the large number of possible conformations and enormous amount of computations required. Tabu search is an iterative heuristic procedure which has been shown to be a remarkably effective method for solving combinatorial optimization problems. In this paper, an algorithm is designed for the cubic lattice model using tabu search. The algorithm has been tested on a chain of 27 monomers. Computational results show that our method outperforms previously reported approaches for the same model.