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A Meta-heuristic Framework for Secondary Protein Structure Prediction using BAT-FLANN Optimization Algorithm

Affiliations

  • Computer Science & Engineering, Institute of Technical Education and Research, Siksha O Anusandhan University, Bhubaneswar - 751030, Odisha, India

Abstract


Background/Objectives: Proteins are the fundamental units of biology; the mechanism by which primary sequence of proteins is predicted into its secondary structure is not yet accurately achieved. Methods/Statistical analysis: In this paper, BAT inspired FLANN (Functional Link Artificial Neural Network) model for protein secondary structure prediction with low computation cost and accuracy has been proposed. The proposed model consists of three different phases; i) First, the primary sequence of amino acid is converted into dynamic matrix for different window sizes then this dynamic matrix is used to derive correlation matrix, ii) Second, FLANN is used to classify each sequence of correlation matrix with different learning parameters and random weights. BAT inspired optimization algorithm has been used to optimize the weight and learning parameters of BAT-FLANN, and (iii) finally, refinement of secondary structure result. Results: Experiments were conducted with real datasets of some primary sequence on RS126 and CB396 datasets. Proposed method has been compared with existing DSC, NNSSP, PHD, PREDATOR, ZPRED, MULPRED, SVM models and found to be more promising. Conclusion/Application: The proposed method achieves average Q3 accuracy 81.2% and 82.7% for CB396 and RS126 dataset respectively. Moreover the segment overlap (SOV) is 76.1% and 75.3% for CB396 and RS126 dataset respectively.

Keywords

BAT-FLANN, Classifier, Dynamic Matrix, Protein Data Bank (PDB), Secondary Structure

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