Prediction of protein secondary structure based on residue pairs.
The GOR program for predicting protein secondary structure is extended to include triple correlation. A score system for a residue pair to be at certain conformation state is derived from the conditional weight matrix describing amino acid frequencies at each position of a window flanking the pair under the condition for the pair to be at the fixed state. A program using this score system to predict protein secondary structure is established. After training the model with a learning set created from PDB_SELECT, the program is tested with two test sets. As a method using single sequence for predicting secondary structures, the approach achieves a high accuracy near 70%.
Interdisciplinary Center of Theoretical Studies, Chinese Academy of Sciences, Beijing 100080, China.
Xin
X
Liu
Li-Mei
LM
Zhang
Wei-Mou
WM
Zheng
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D016000:Cluster Analysis; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
D000596:Amino Acids; D011506:Proteins