Before revision:  The computing speed is not nearly enough to simulate the atom-level fold process when computing the physical energy among all the atoms. The two obstacles can be removed by knowledge-based methods, which combine knowledge learned from the known structures and biologists  knowledge of the folding process of protein or RNA. In the dissertation, I will present my results in building a knowledge-based method by using machine learning methods to tackle this problem.
After revision:  The two obstacles can be removed by knowledge-based methods, which combine knowledge learned from the known structures and biologists knowledge of the folding process of protein or RNA. In the dissertation, I will present my results in building a knowledge-based method by using machine learning methods to tackle this problem.