Research Article Extracting Physicochemical Features to Predict Protein Secondary Structure

License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. We propose a protein secondary structure prediction method based on position-specific scoring matrix (PSSM) profiles and four physicochemical features including conformation parameters, net charges, hydrophobic, and side chain mass. First, the SVM with the optimal window size and the optimal parameters of the kernel function is found.Then,we train the SVMusing the PSSMprofiles generated fromPSI-BLAST and the physicochemical features extracted from theCB513 data set. Finally, we use the filter to refine the predicted results from the trained SVM. For all the performance measures of our method