Cooling schedules for optimal annealing
Mathematics of Operations Research
On the complexity of string folding
Discrete Applied Mathematics - Special volume on computational molecular biology
On the convergence of generalized hill climbing algorithms
Discrete Applied Mathematics
Local Search in Combinatorial Optimization
Local Search in Combinatorial Optimization
SIAM Review
Protein Conformation of a Lattice Model Using Tabu Search
Journal of Global Optimization
A complete and effective move set for simplified protein folding
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Approximate protein folding in the HP side chain model on extended cubic lattices
Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Long proteins with unique optimal foldings in the H-P model
Computational Geometry: Theory and Applications - Special issue: The European workshop on computational geometry -- CG01
Opportunities for Combinatorial Optimization in Computational Biology
INFORMS Journal on Computing
Application of tabu search strategy for finding low energy structure of protein
Artificial Intelligence in Medicine
Evaluating protein structure-prediction schemes using energy landscape theory
IBM Journal of Research and Development
Stochastic protein folding simulation in the three-dimensional HP-model
Computational Biology and Chemistry
A Local Move Set for Protein Folding in Triangular Lattice Models
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
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We present results from two- and three-dimensional protein folding simulations in the HP-model on selected benchmark problems. The importance of the HP-model for investigating general complexity issues of protein folding has been recently demonstrated by Fu & Wang (LNCS 3142:630-644, 2004) in proving an exp(O(n1-1/d ċ ln n)) time bound for d-dimensional protein folding simulation of sequences of length n. The time bound is close to the approximation of real folding times of exp(λ ċ n2/3 ± Χ ċ n1/2/2)ns by Finkelstein & Badretdinov (FOLD DES 2:115-121, 1997), where λ and Χ are constants close to unity. We utilise a stochastic local search procedure that is based on logarithmic simulated annealing. We obtain that after (m/δ)a.D Markov chain transitions the probability to be in a minimum energy conformation is at least 1 - δ, where m ≤ b(d) ċ n is the maximum neighbourhood size for a small integer b(d), 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 sequence-specific, and we conjecture D n1 -1/d as a worst case upper bound. We analyse D n1-1/d experimentally on selected HP-model benchmark problems.