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Approximation Algorithms for Three Dimensional Protein Folding

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WALCOM: Algorithms and Computation (WALCOM 2016)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9627))

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Abstract

Predicting protein secondary structures using lattice models is one of the most studied computational problems in bioinformatics. Here the secondary structure or three dimensional structure of a protein is predicted from its amino acid sequence. The secondary structure refers to local sub-structures of a protein. Mostly founded secondary structures are alpha helix and beta sheets. Simplified energy models have been proposed in the literature on the basis of interaction of amino acid residues in proteins. Here we use well researched Hydrophobic-Polar (HP) energy model. In this paper, we propose the hexagonal prism lattice with diagonals that can overcome the problems of other lattice structures, e.g., parity problem. We give two approximation algorithms for protein folding on this lattice. Our first algorithm leads us to a similar structure of helix structure that is commonly found in a protein structure. This motivates us to propose the next algorithm with a better approximation ratio.

M.S. Rahman—Supported by a ACU Titular Fellowship.

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Authors and Affiliations

  1. ALEDA Group, Department of CSE, BUET, Dhaka, 1205, Bangladesh

    Dipan Lal Shaw, Shuvasish Karmaker & M. Sohel Rahman

  2. University of California, Riverside, CA, 92521, USA

    Dipan Lal Shaw

  3. Department of Computational Engineering and Science, McMaster University, Hamilton, ON, Canada

    A. S. M. Shohidull Islam

Authors
  1. Dipan Lal Shaw
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  2. A. S. M. Shohidull Islam
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  3. Shuvasish Karmaker
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  4. M. Sohel Rahman
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Correspondence to Dipan Lal Shaw .

Editor information

Editors and Affiliations

  1. Dept. of Computer Science and Engin., Bangladesh Univ. of Engin. & Technol., Dhaka, Bangladesh

    Mohammad Kaykobad

  2. Dept. of Computer Science, Sapienza University of Rome, Rome, Italy

    Rossella Petreschi

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Shaw, D.L., Islam, A.S.M.S., Karmaker, S., Rahman, M.S. (2016). Approximation Algorithms for Three Dimensional Protein Folding. In: Kaykobad, M., Petreschi, R. (eds) WALCOM: Algorithms and Computation. WALCOM 2016. Lecture Notes in Computer Science(), vol 9627. Springer, Cham. https://doi.org/10.1007/978-3-319-30139-6_22

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  • DOI: https://doi.org/10.1007/978-3-319-30139-6_22

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-30138-9

  • Online ISBN: 978-3-319-30139-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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