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Protein folding problem is one of the most important problems in bioinformatics, and hydrophobic polar model is a wide abstract model in study of this problem. Simulated annealing is a heuristic global optimization algorithm, which has been successfully applied to many difficult optimization problems. This paper proposes an improved simulated annealing algorithm to search the ground state of HP lattice...
Using a triangular lattice model to study the designability of protein folding, we overcame the parity problem of previous cubic lattice model and enumerated all the sequences and compact structures on a simple two-dimensional triangular lattice model of size 4+5+6+5+4. We used two types of amino acids, hydrophobic and polar, to make up the sequences, and achieved 223+212 different sequences excluding...
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