A Novel Framework for Ab Initio Coarse Protein Structure Prediction

Advances in Bioinformatics
Sandhya Parasnath DubeyM Sathish Kumar

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 probability-based selection operators that limit the local convergence; (iii) use of secondary structure based mutation operator that makes the structure more 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 de...Continue Reading

References

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Citations

May 7, 2021·Journal of Biomolecular Structure & Dynamics·Varanavasi Nallasamy, Malarvizhi S

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Methods Mentioned

BETA
Nuclear
X-ray
protein folding

Software Mentioned

ERS
HGA
AMBER
EDA
HHGA
OSSGA
Visual C
GA
OpenGL graphics
Fasta

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