Ensemble model for accuracy prediction of protein secondary structure

Srushti C. Shivaprasad, Prathibhavani P. Maruthi, Teja Shree Venkatesh, Venugopal K. Rajuk


Predicting a protein’s secondary structure is crucial for understanding the working of proteins. Despite advancements over the years, the top predictors have achieved only 80% Q8 accuracy when sequence profile information is the sole input. An ensemble approach is proposed using convolutional neural network (CNN) and a classifier known as support vector machine (SVM) on both the partial and the whole CullPDB datasets. The protein secondary structure (PSS) has a complex hierarchical structure, as well as the ability to take into account the reliance between neighbouring labels. A detailed experiment yielding high levels of Q8 accuracy with scores of 97.91%, 85.13%, and 78.02% using 20%, 80%, and 100% respectively of the protein residues on the new predicted dataset CullPDB6133 which is better than the accuracies predicted by similar models. The proposed methodology highlights the use of CNN as a general framework, for efficiently predicting eight-state (Q8) accuracy of secondary protein structures with a low time and space complexity.


Convolutional neural networks; CullPDB6133; Protein secondary structure prediction; Q8 accuracy; SVM classifier

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DOI: http://doi.org/10.11591/ijeecs.v32.i3.pp1664-1677


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The Indonesian Journal of Electrical Engineering and Computer Science (IJEECS)
p-ISSN: 2502-4752, e-ISSN: 2502-4760
This journal is published by the Institute of Advanced Engineering and Science (IAES) in collaboration with Intelektual Pustaka Media Utama (IPMU).

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