In the current study, to further advance the prediction accuracy and understand the binding mechanism of DNA-protein interaction, we presented here a novel encoding method called PSSM distance transformation (PSSM-DT) to transform the PSSM profiles of query sequences into uniform numeric representations. Then we constructed a DNA-binding protein identification method SVM-PSSM-DT by combining the PSSM-DT with SVM. The benchmark test and independent test showed that PSSM-DT is a promising protein encoding method.