3D-structure Modeling for Regular Segments of Low Homology Unknown Structure Protein

As it is difficult to find similar structure protein segments from PDB database to model 3D structure for unknown structure protein of low homology, protein secondary structure prediction software and BLAST are applied in this paper to model regular segments for low homology unknown structure protein (alpha-Helix, beta-Strand). First, protein secondary structure prediction software is adopted to extract secondary structures for unknown structure proteins. Then, by BLAST, main chain configuration of regular segments can be modeled by comparative modeling and adjustment. Finally, regular segments are predicted for several neurotoxins, which illustrates the effectiveness of the proposed method.