Optimal HP configurations of proteins by combining local search with elastic net algorithm |
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| Institution: | 1. Ospedali Riuniti University Hospital, Foggia, Italy;2. Department of Medical & Surgical Sciences, University of Foggia, Italy;1. Duke University School of Medicine, Durham, NC;2. Division of Cardiology, Duke University School of Medicine, Durham, NC;3. Duke Clinical Research Institute, Durham, NC;4. Department of Medicine, University of Mississippi, Jackson, MS;5. Section of Cardiovascular Medicine, Yale University School of Medicine and the Yale New Haven Hospital, New Haven, CT;1. College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China;2. The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China;3. Department of Anesthesiology, Harbin Medical University Cancer Hospital, Harbin 150081, China;4. Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mingolia Wesure Date Technology Co., Ltd., Hohhot 010010, China |
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| Abstract: | The prediction of protein conformation from its amino-acid sequence is one of the most prominent problems in computational biology. But it is NP-hard. Here, we focus on an abstraction widely studied of this problem, the two-dimensional hydrophobic-polar protein folding problem (2D HP PFP). Mathematical optimal model of free energy of protein is established. Native conformations are often sought using stochastic sampling methods, but which are slow. The elastic net (EN) algorithm is one of fast deterministic methods as travelling salesman problem (TSP) strategies. However, it cannot be applied directly to protein folding problem, because of fundamental differences in the two types of problems. In this paper, how the 2D HP protein folding problem can be framed in terms of TSP is shown. Combination of the modified elastic net algorithm and novel local search method is adopted to solve this problem. To our knowledge, this is the first application of EN algorithm to 2D HP model. The results indicate that our approach can find more optimal conformations and is simple to implement, computationally efficient and fast. |
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