Title of article :
Relating time complexity of protein folding simulation to approximations of folding time Original Research Article
Author/Authors :
K. Steinh?fel، نويسنده , , A. Skaliotis، نويسنده , , A.A. Albrecht، نويسنده ,
Issue Information :
دوهفته نامه با شماره پیاپی سال 2007
Pages :
6
From page :
465
To page :
470
Abstract :
Finkelstein and Badretdinov [A.V. Finkelstein, A.Y. Badretdinov, Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold, Fold. Des. 2 (1997) 115–121] approximated the folding time of protein sequences of length n by image, where λ and χ are constants close to unity. Recently, Fu and Wang [B. Fu, W. Wang, A image time algorithm for d-dimensional protein folding in the HP-model, in: J. Daz, J. Karhumäki, A. Lepistö, D. Sannella (Eds.), Proceedings of the 31st International Colloquium on Automata, Languages and Programming, in: Lecture Notes in Comput. Sci., vol. 3142, Springer-Verlag, Heidelberg, 2004, pp. 630–644] published an image algorithm for d-dimensional protein folding simulation in the HP-model, which is close to the folding time approximation by Finkelstein and Badretdinov and can be seen as a justification of the HP-model for investigating general complexity issues of protein folding. We propose a stochastic local search procedure that is based on logarithmic simulated annealing. We obtain that after image Markov chain transitions the probability to be in a minimum energy conformation is at least image, where image is the maximum neighbourhood size (image small integer), a is a small constant, and D is the maximum value of the minimum escape height from local minima of the underlying energy landscape. We note that the time bound is instance-specific, and we conjecture image as a worst case upper bound. We analyse image experimentally on selected benchmark problems for the image case.
Keywords :
protein folding , HP-model , Landscape analysis , Stochastic local search , Simulated annealing
Journal title :
Computer Physics Communications
Serial Year :
2007
Journal title :
Computer Physics Communications
Record number :
1137178
Link To Document :
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