Because it is hard to search similar structure for low similarity unknown structure proteins dimefly from the Protein Data Bank(PDB)database,3D-structure is modeled in this paper for secondary structure regular fragments(α-Helices,β-Strands)of such proteins by the protein secondary structure prediction software,the Basic Local Alignment Search Tool(BLAST)and the side chain construction software SCWRL3.First.the protein secondary structure prediction software is adopted to extract secondary structure fragments from the unknown structure proteins.Then.regular fragments are regulated by BLAST based on comparative modeling,providing main chain configurations.Finally,SCWRL3 is applied to assemble side chains for regular fragments,so that 3D-structure of regular fragments of low similarity un known structure protein is obtained.Regular fragments of several neurotoxins ale used for test.Simulation results show that the prediction errors are less than 0.06nm for regular fragments less than 10 amino acids,implying the simpleness and effectiveness of the proposed method.