A Novel Offspring Selection Strategy in GAs for Protein Structure Prediction

Su, Shih Chieh; Tsay, Jyh Jong

doi:10.1109/is3c.2014.304

Cited by 2 publications

(1 citation statement)

References 32 publications

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“…For triangular lattice, this study has been carried out using benchmark sequences taken from the work of Islam and Chetty [ 47 ]. In this implementation, we have compared the performance of MA(EP+HC) with HGA [ 48 ], ERS-GA [ 39 ], HHGA [ 39 ], TS [ 49 ], CMA [ 47 ], and OSSGA [ 40 ] and results are summarized in Table 5 . It has been observed that the MA(EP+HC) has obtained the lowest free energy ( Table 5 ) for the test sequence in experiment compared to the previous state-of-the-art approaches.…”

Section: Resultsmentioning

confidence: 99%

A Novel Framework for Ab Initio Coarse Protein Structure Prediction

Dubey

Balaji

Kini

et al. 2018

Advances in Bioinformatics

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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 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.

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Section: Resultsmentioning

confidence: 99%

A Novel Framework for Ab Initio Coarse Protein Structure Prediction

Dubey

Balaji

Kini

et al. 2018

Advances in Bioinformatics

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Hps_psp: High Performance System for Protein Structure Prediction

2019

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Prediction of least energy conformation of a protein from its primary structure (chain of amino acids) is an optimization problem associated with a large complex energy landscape. In this study, a simple 2D hydrophobic–hydrophilic model was used to model the protein sequence, which allows the fast and efficient design of genetic algorithm-based protein structure prediction approach. The neighborhood search strategy is integrated into the genetic operator. The neighborhood search guides the genetic operator to regions in the computational space with good solutions. To prevent convergence to local optima, the proposed method employs crowding-based parent replacement strategy, which improves the performance of the algorithm and the ability to deal with multiple numbers of solutions. The proposed algorithm was tested with a standard benchmark of HP sequences and comparative results demonstrate that the proposed system beats most of the evolutionary algorithms for seven sequences. It finds the best energy for a sequence of length [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text].

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A Novel Offspring Selection Strategy in GAs for Protein Structure Prediction

Cited by 2 publications

References 32 publications

A Novel Framework for Ab Initio Coarse Protein Structure Prediction

A Novel Framework for Ab Initio Coarse Protein Structure Prediction

Hps_psp: High Performance System for Protein Structure Prediction

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