Cooling schedules for optimal annealing
Mathematics of Operations Research
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
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
Hi-index | 0.00 |
The hydrophobic-hydrophilic (H-P) model for protein folding was introduced by Dill et al.[7]. A problem instance consists of a sequence of amino acids, each labeled as either hydrophobic (H) or hydrophilic (P). The sequence must be placed on a 2D or 3D grid without overlapping, so that adjacent amino acids in the sequence remain adjacent in the grid. The goal is to minimize the energy, which in the simplest variation corresponds to maximizing the number of adjacent hydrophobic pairs. The protein folding problem in the H-P model is NP-hard in both 2D and 3D. Recently, Fu and Wang [10] proved an exp(O(n1−−1/d)ln n) algorithm for d-dimensional protein folding simulation in the HP-model. Our preliminary results on stochastic search applied to protein folding utilize complete move sets proposed by Lesh et al.[15] and Blazewicz et al.[4]. We obtain that after (m/δ)O( Γ) Markov chain transitions, the probability to be in a minimum energy conformation is at least 1–δ, where m is the maximum neighbourhood size and Γ is the maximum value of the minimum escape height from local minima of the underlying energy landscape. We note that the time bound depends on the specific instance. Based on [10] we conjecture Γ≤n1−−1/d. We analyse $\Gamma \leq \sqrt{n}$ experimentally on selected benchmark problems [15,21] for the 2D case.