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Record-to-Record Travel Algorithm for Biomolecules Structure Prediction

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Computational Science and Its Applications – ICCSA 2021 (ICCSA 2021)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 12949))

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Abstract

The biomolecules structure prediction problem (BSP) - especially the protein structure prediction (PSP) and the nucleic acids structure prediction - was introduced in the computational biology field approximately 45–50 years ago. The PSP on hydrophobic-polar lattice model (HP model) is a combinatorial optimisation problem, and consists in aims to minimize an arbitrary energy function associated with every native structure.

To solve the PSP problem, many metaheuristic methods were applied. Although the record-to-record travel algorithm (RRT) has proven useful in solving combinatorial optimisation problems, it has not been applied so far to solve the PSP problem.

In this paper, a mathematical modeling for PSP on the 2D HP rectangular lattice is developed and an adapted record-to-record travel algorithm (aRRT) is applied to address the combinatorial optimisation problem. For candidate solutions perturbation, a rotation and a diagonal move mutation operators were used.

A benchmark data set is used to test the RRT algorithm. The results obtained show that the algorithm is competitive when compared to the best published results. The main advantage of the RRT algorithm is that it is time-efficient, and requires small computational resources to obtain the same results as swarm intelligence algorithms.

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Acknowledgment

The authors would like to thank Prof. Univ. Dr. Bazil Parv for his professional guidance and valuable support.

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Authors and Affiliations

  1. Babes-Bolyai University, 400084, Cluj-Napoca, Romania

    Ioan Sima & Daniela-Maria Cristea

Authors
  1. Ioan Sima
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  2. Daniela-Maria Cristea
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Corresponding author

Correspondence to Ioan Sima .

Editor information

Editors and Affiliations

  1. University of Perugia, Perugia, Italy

    Osvaldo Gervasi

  2. University of Basilicata, Potenza, Potenza, Italy

    Beniamino Murgante

  3. Covenant University, Ota, Nigeria

    Sanjay Misra

  4. University of Cagliari, Cagliari, Italy

    Chiara Garau

  5. University of Cagliari, Cagliari, Italy

    Ivan Blečić

  6. Monash University, Clayton, VIC, Australia

    David Taniar

  7. Kyushu Sangyo University, Fukuoka, Japan

    Bernady O. Apduhan

  8. University of Minho, Braga, Portugal

    Ana Maria A. C. Rocha

  9. Polytechnic University of Bari, Bari, Italy

    Eufemia Tarantino

  10. Polytechnic University of Bari, Bari, Italy

    Carmelo Maria Torre

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Sima, I., Cristea, DM. (2021). Record-to-Record Travel Algorithm for Biomolecules Structure Prediction. In: Gervasi, O., et al. Computational Science and Its Applications – ICCSA 2021. ICCSA 2021. Lecture Notes in Computer Science(), vol 12949. Springer, Cham. https://doi.org/10.1007/978-3-030-86653-2_33

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  • DOI: https://doi.org/10.1007/978-3-030-86653-2_33

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-86652-5

  • Online ISBN: 978-3-030-86653-2

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