Simulated annealing: theory and applications
Simulated annealing: theory and applications
Global optimization
Genetic algorithms + data structures = evolution programs (3rd ed.)
Genetic algorithms + data structures = evolution programs (3rd ed.)
Genetic Algorithms in Search, Optimization and Machine Learning
Genetic Algorithms in Search, Optimization and Machine Learning
Meta-Heuristics: Theory and Applications
Meta-Heuristics: Theory and Applications
Local Search in Combinatorial Optimization
Local Search in Combinatorial Optimization
Tabu Search
Meta-Heuristics: Advances and Trends in Local Search Paradigms for Optimization
Meta-Heuristics: Advances and Trends in Local Search Paradigms for Optimization
Stochastic Local Search: Foundations & Applications
Stochastic Local Search: Foundations & Applications
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In this paper, we propose a new method for protein structure prediction based on the mini-threading approach. It has two main components, relevant protein fragment retrieval and protein 3-D structure construction. First, we develop new computational techniques to identify useful fragments in Protein Data Bank (PDB) for a given query protein. Then, different from the angular restraints used in most existing mini-threading methods, we formulate spatial restraints derived from the alignments between a query sequence and its fragment hits of known structures in Cartesian coordinates. We include additional information for the scoring function, such as pair-wise contact potential and apply classical multidimensional scaling method for 3-D structure construction. The structure is further refined by local optimization algorithms. The new method represents a novel framework that can utilize the information in the known protein structure database more effectively and efficiently than existing methods.