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Identifying Secondary structure of protein becomes more important in designing drugs. Presently, machine learning algorithms like Artificial Neural Network (ANN) and Support Vector Machine (SVM) has been utilized to identify the Protein Secondary Structure (PSS). However, in order to improve more accuracy of PSS prediction, this work proposed PSO to search the best parameters of theANN predictor developed for QscR protein. From the results, it is found that the proposed topologyexhibits high accuracy than the other existing techniques.