A Balanced Secondary Structure Predictor

• Main Author: Islam, Md Nasrul
• Format: Others
• Published: ScholarWorks@UNO 2015
• Subjects: Protein; Secondary structure; MetaSSPred; Support vector machine; Genetic algorithm; Balanced prediction; Other Computer Engineering
• Online Access: http://scholarworks.uno.edu/td/1995; http://scholarworks.uno.edu/cgi/viewcontent.cgi?article=3100&context=td

Secondary structure (SS) refers to the local spatial organization of the polypeptide backbone atoms of a protein. Accurate prediction of SS is a vital clue to resolve the 3D structure of protein. SS has three different components- helix (H), beta (E) and coil (C). Most SS predictors are imbalanced as their accuracy in predicting helix and coil are high, however significantly low in the beta. The objective of this thesis is to develop a balanced SS predictor which achieves good accuracies in all three SS components. We proposed a novel approach to solve this problem by combining a genetic algorithm (GA) with a support vector machine. We prepared two test datasets (CB471 and N295) to compare the performance of our predictors with SPINE X. Overall accuracy of our predictor was 76.4% and 77.2% respectively on CB471 and N295 datasets, while SPINE X gave 76.5% overall accuracy on both test datasets.