Use of tetrapeptide signals for protein secondary-structure prediction

This paper develops a novel sequence-based method, tetra-peptide-based increment of diversity with quadratic discriminant analysis (TPIDQD for short), for protein secondary-structure prediction. The proposed TPIDQD method is based on tetra-peptide signals and is used to predict the structure of the central residue of a sequence fragment. The three-state overall per-residue accuracy (Q(3)) is about 80% in the threefold cross-validated test for 21-residue fragments in the CB513 dataset. The accuracy can be further improved by taking long-range sequence information (fragments of more than 21 residues) into account in prediction. The results show the tetra-peptide signals can indeed reflect some relationship between an amino acid's sequence and its secondary structure, indicating the importance of tetra-peptide signals as the protein folding code in the protein structure prediction.