Optimal HP configurations of proteins by combining local search with elastic net algorithm

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). Mathemati...

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Bibliographic Details
Published in:Journal of biochemical and biophysical methods 2007-04, Vol.70 (3), p.335-340
Main Authors: Guo, Yu-Zhen, Feng, En-Min, Wang, Yong
Format: Article
Language:English
Subjects:
2D HP lattice model
Algorithms
Biophysical Phenomena
Biophysics
Elastic net algorithm
Elasticity
Hydrophobic and Hydrophilic Interactions
Local search method
Models, Molecular
Protein Folding
Protein folding problem
Proteins - chemistry
Thermodynamics
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Summary: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.
ISSN:0165-022X
1872-857X
DOI:10.1016/j.jbbm.2006.08.001