| Now, the forecasting 3D space structure of the biology protein is the focus in biology domain. The protein folding structure has determined it's biological function to a great extent, and the 3D space structure of the protein has determined the function of protein biological function. In order to know the biological function of the biology in detail, we must far study the 3D space structure of the protein, and afford a efficient algorithm to describe the space structure of the protein form the case of study at last.There is tow kinds of aminophenol in the protein sequence, the one is hydrophobe aminophenol, the other is hydrophile aminophenol. The characteristic in the aminophenol is be showed: the hydrophile aminophenol is be closed as soon as possible. Many scholars afford the some models and algorithms by the characteristics. By comparing and analyzing the algorithm in existence, I find the only disperse model be used in the algorithm. Although the disperse model is beautiful and sententiously, the problem is NP-hard problem, when the number of aminophenol is very huge, the style of the difficulty of settle the problem is exponential, solving the problem is impossible. So the model and algorithm in existence has disadvantages in describing and solving the protein folding problem.In order to optimizing the algorithm about the protein folding, there is a new algorithm by enlightening about the formerly algorithm. The algorithm afford the corresponding physical model of the math model by the method named simulating nature and give the precision math expressions of the model .In all test cases,so we find a kind of far efficiency algorithm of calculating the protein structure in globe area through researching the physical model and figuring the math expressions by using the algorithm about calculating the right result and a kind of optimizing method. It takes a characteristic of efficiently find the result close to the best in globe area.
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