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, Harshad R. Kavathiyal

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish
Pages (from-to)149-155
Number of pages7
JournalAsian Journal of Biochemistry
Volume11
Issue number3
DOIs
Publication statusPublished - 2016

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Conformations
Proteins
Anethum graveolens
Benchmarking
Protein Conformation
Computational Biology
Databases
Research

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Biochemistry, medical

Cite this

Dubey, Sandhya P.N. ; Gopalakrishna Kini, N. ; Sathish Kumar, M. ; Balaji, S. ; Sumana Bhat, M. P. ; Kavathiyal, Harshad R. / A novel conformation generation framework for de novo protein structure prediction using hydrophobic-polar model. In: Asian Journal of Biochemistry. 2016 ; Vol. 11, No. 3. pp. 149-155.
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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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A novel conformation generation framework for de novo protein structure prediction using hydrophobic-polar model. / Dubey, Sandhya P.N.; Gopalakrishna Kini, N.; Sathish Kumar, M.; Balaji, S.; Sumana Bhat, M. P.; Kavathiyal, Harshad R.

In: Asian Journal of Biochemistry, Vol. 11, No. 3, 2016, p. 149-155.

Research output: Contribution to journalArticle

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AU - Gopalakrishna Kini, N.

AU - Sathish Kumar, M.

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AU - Sumana Bhat, M. P.

AU - Kavathiyal, Harshad R.

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