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Evolutionary Algorithms for the Inverse Protein Folding Problem

In: Handbook of Heuristics

Author

Listed:
  • Sune S. Nielsen

    (University of Luxembourg, Computer Science and Communications (CSC) Research Unit, FSTC)

  • Grégoire Danoy

    (University of Luxembourg, Computer Science and Communications (CSC) Research Unit, FSTC)

  • Wiktor Jurkowski

    (The Genome Analysis Centre (TGAC), Norwich Research Park)

  • Roland Krause

    (University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB))

  • Reinhard Schneider

    (University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB))

  • El-Ghazali Talbi

    (INRIA Lille Nord Europe, Université des sciences et technologies de Lille)

  • Pascal Bouvry

    (University of Luxembourg, Computer Science and Communications (CSC) Research Unit, FSTC)

Abstract

Protein structure prediction is an essential step in understanding the molecular mechanisms of living cells with widespread application in biotechnology and health. The inverse folding problem (IFP) of finding sequences that fold into a defined structure is in itself an important research problem at the heart of rational protein design. In this chapter, a multi-objective genetic algorithm (MOGA) using the diversity-as-objective (DAO) variant of multi-objectivization is presented, which optimizes the secondary structure similarity and the sequence diversity at the same time and hence searches deeper in the sequence solution space. To validate the final optimization results, a subset of the best sequences was selected for tertiary structure prediction. Comparing secondary structure annotation and tertiary structure of the predicted model to the original protein structure demonstrates that relying on fast approximation during the optimization process permits to obtain meaningful sequences.

Suggested Citation

  • Sune S. Nielsen & Grégoire Danoy & Wiktor Jurkowski & Roland Krause & Reinhard Schneider & El-Ghazali Talbi & Pascal Bouvry, 2025. "Evolutionary Algorithms for the Inverse Protein Folding Problem," Springer Books, in: Rafael Martí & Panos M. Pardalos & Mauricio G.C. Resende (ed.), Handbook of Heuristics, edition 0, chapter 41, pages 1295-1319, Springer.
    • Handle: RePEc:spr:sprchp:978-3-032-00385-0_59
    DOI: 10.1007/978-3-032-00385-0_59
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