Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures

The major obstacles to predicting the native structure of a protein using molecular dynamics simulation are the error in the potential energy function and the large amount of time required for simulation. Here, we demonstrated that these problems could be greatly alleviated by just imposing restraints on the backbone dihedral angles of the residues that have secondary structures in the native structure. We applied this method to a 28-residue protein, FSD-EY, and showed that its native tertiary structure was accurately predicted as a structure that had the lowest free-energy in the conformational subspace in which the native secondary structures were formed.