The application of the protein design method based on the HNP model and the relative entropy theory is discussed for four structural classes of real proteins, and the results are compared with that of the HP model. Testing on 190 proteins shows that this method is generally effective for the different structural classes of proteins. Further studies show that the success rate of this method on regular secondary structures is higher than that on the random coil. Additionally, the success rate for different types of amino acids is also analyzed. It is found that the success rate on the hydrophilic residues is higher than those of the other two types. Furthermore, the success rate of this method on the conserved residues is higher than the non-conserved residues. The reasons resulting in the difference of the success rate on different systems were also analyzed. All analyses mentioned above make the foundation for the development and the application of this method in the future.

Twenty kinds of amino acids are simplified into 3 types: hydrophobic amino acids (H), hydrophilic amino acids (P) and neutral amino acids (N). Each residue is reduced to a bead which locates in the position of the C?琢 atom. The off-lattice model is adopted and the relative entropy is used as a minimization function to predict the tertiary structure of a protein. A new contact intensity function is given to consist with protein design research based on the relative entropy. Testing on several real proteins from Protein Data Bank (PDB) shows the good results obtained with the model and method. The root mean square deviations (RMSD) of the predicted structures relative to the native structures range from 0.30 to 0.70 nm. A foundation for studying protein design using the HNP model and the relative entropy was made.

Protein-protein interactions and recognition are the focal and hot themes of the life science field in the 21st century. Molecular docking approach is the effective computer modeling technology in the study of this topic. Generally, the protein-protein docking procedure is composed of four stages: searching of the binding modes of the receptor and the ligand, filtering of docked modes to eliminate the irrational docked structures, optimizing the structures, evaluating the docked modes with the refined scoring function and ranking them to obtain the near-native structures. Combining the research group's works, in terms of the international and national progress of protein-protein docking approaches, the detailed review was made about the four stages mentioned above. Additionally, the existing major questions are analyzed and the prospects of the future study are made.