NDLI: A Tabu Search Algorithm for the Protein Folding Problem

Content Provider	IEEE Xplore Digital Library
Author	Mao Chen Chao Yu Jiagang Ouyang
Copyright Year	2009
Abstract	Protein folding problem is one of the central problems in the cross-discipline field involving biology, computational physics and computer science. In this paper, based on the heuristic physical model, a three-dimensional AB mode-based protein folding problem is converted from a nonlinear constraint-satisfied problem to an unconstrained optimization problem, which can be solved by the gradient method. However, in the course of solution using the gradient method, it is often possible for the calculation of gradient method to fall into the trap of local minimum. To jump out of the trap of local minimum and guide the search to the points with better prospects, we proposed a heuristic Tabu search method. The computational results show that our algorithm can outperform nPERM algorithm and HSA algorithm in terms of finding states with lower energy for the four benchmark sequences.
Starting Page	237
Ending Page	240
File Size	329613
Page Count	4
File Format	PDF
ISBN	9780769538655
DOI	10.1109/ISCID.2009.66
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-12-12
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Gradient methods Sequences Biological system modeling gradient method Proteins Computer science Constraint optimization Physics computing Search methods Tabu search Biology computing protein folding AB off-lattice model Computational biology
Content Type	Text
Resource Type	Article

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