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Asian Journal of Biochemistry

Year: 2016  |  Volume: 11  |  Issue: 3  |  Page No.: 149 - 155

A Novel Conformation Generation Framework for De novo Protein Structure Prediction Using Hydrophobic-Polar Model

Sandhya P.N. Dubey, N. Gopalakrishna Kini, M. Sathish Kumar, S. Balaji, M.P. Sumana Bhat and Harshad R. Kavathiyal

Abstract

Background and Objective: The Protein Structure Prediction (PSP) problem is one of the hardest problems in computational biology and technological research. To reduce the complexity of the problem, Dill proposed the Hydrophobic-Polar (HP) model which subsequently became a major tactic to the PSP problem. Methodology: In this study, a novel algorithm was proposed to solve the PSP problem using Dill’s HP model. Here, protein conformation is modeled with square and triangular lattice. The proposed method is tested on a set of benchmark sequences and real protein sequence 4RXN taken from Protein Data Bank (PDB). Results: It is observed that, the proposed approach results in good quality conformation in term of hydrophobic contact with 89% of accuracy. Also, experimental results show that the structure modeled with triangular lattice is closer to the wet lab structure. Conclusion: Results indicate that the proposed approach is promising to generate good number HP conformation, with immense drop in time.

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