We use a gapped structural threading method to predict the protein conformations in solution. After analysis of the results in CASP6 (Critical Assessment of Techniques for Protein Structure Prediction), we found there are some weak points in the scoring function which we should refine. We made three attempts to improve the scoring function. First we automatically adjusted the 20 parameters of residue-residue interactions. Then we investigate 29 contact matrix potentials, in order to select the best one for energy evaluation. Last, we add the Blosum Matrix score in our energy function to take account of the sequence similarity information in consideration.