A Novel Framework for Ab Initio Coarse Protein Structure Prediction

Dubey, Sandhya P and Balaji, S and Kini, Gopalakrishna N and Sathish, Kumar (2018) A Novel Framework for Ab Initio Coarse Protein Structure Prediction. Advances in Bioinformatics. 01-17. ISSN 1687-8027

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Abstract

Hydrophobic-Polar model is a simplified representation of Protein Structure Prediction (PSP) problem. However, even with the HP model, the PSP problem remains NP-complete. This work proposes a systematic and problem specific design for operators of the evolutionary program which hybrids with local search hill climbing, to efficiently explore the search space of PSP and thereby obtain an optimum conformation. The proposed algorithm achieves this by incorporating the following novel features: (i) new initialization method which generates only valid individuals with (rather than random) better fitness values; (ii) use of probabilitybased selection operators that limit the local convergence; (iii) use of secondary structure based mutation operator that makes the structuremore closely to the laboratory determined structure; and (iv) incorporating all the above-mentioned features developed a complete two-tier framework.The developed framework builds the protein conformation on the square and triangular lattice.The test has been performed using benchmark sequences, and a comparative evaluation is done with various state-of-the-art algorithms. Moreover, in addition to hypothetical test sequences, we have tested protein sequences deposited in protein database repository. It has been observed that the proposed framework has shown superior performance regarding accuracy (fitness value) and speed (number of generations needed to attain the final conformation).The concepts used to enhance the performance are generic and can be used with any other population-based search algorithm such as genetic algorithm, ant colony optimization, and immune algorithm

Item Type: Article
Uncontrolled Keywords: Protein Structure Prediction; genetic algorithm; HP approach
Subjects: Engineering > MIT Manipal > Biotechnology
Engineering > MIT Manipal > Computer Science and Engineering
Engineering > MIT Manipal > Electronics and Communication
Depositing User: MIT Library
Date Deposited: 03 Jul 2018 09:57
Last Modified: 03 Jul 2018 09:57
URI: http://eprints.manipal.edu/id/eprint/151461

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