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In silico Maturation: Processing Sequences to Improve Biopolymer Functions Based on Genetic Algorithms

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Applications of Metaheuristics in Process Engineering

Abstract

Peptide ligands and oligonucleotide aptamers are promising agents in therapeutic and diagnostic applications. Conventional technologies to develop these biopolymers depend on screening of functional sequences from a combinatorial library. Because the relationship between a biopolymer sequence and its function is a complex and multidimensional problem, identification of sequences for a desired function cannot be readily accomplished only by rational approaches. To solve such problems, genetic algorithms (GAs) represent an intelligent strategy to perform random search in a defined sequence space. This methodology permits progressive exploration of the sequence space and evolving biopolymer functions. In this chapter, we present an overview of GA-based approaches to develop functional peptide ligands and oligonucleotide aptamers. We review recent trends in GA-based optimization of biopolymer sequences to improve targeted functions.

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Acknowledgments

This work was supported by the Industrial Technology Research Grant Program 2009 of the New Energy and Industrial Technology Development Organization of Japan (NEDO) and a grant from the Low-Carbon Research Network Japan (LCnet). N.S. was supported by Research Fellowships for Young Scientists DC1 from Japan Society for the Promotion of Science.

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Authors and Affiliations

  1. Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho Koganei, Tokyo, 184-8588, Japan

    Nasa Savory, Koichi Abe & Kazunori Ikebukuro

  2. Tokyo University of Technology, 1404-1 Katakuramachi Hachioji, Tokyo, 192-0982, Japan

    Wataru Yoshida

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  1. Nasa Savory
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  2. Koichi Abe
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  3. Wataru Yoshida
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  4. Kazunori Ikebukuro
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Correspondence to Kazunori Ikebukuro .

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  1. Evol. Comput. & Image Proc. Group, Center for Develop. of Adv. Computing, Pune, India

    Jayaraman Valadi

  2. Lab. LiSSi (EA 3956), Université Paris-Est Créteil, Créteil, France

    Patrick Siarry

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Savory, N., Abe, K., Yoshida, W., Ikebukuro, K. (2014). In silico Maturation: Processing Sequences to Improve Biopolymer Functions Based on Genetic Algorithms. In: Valadi, J., Siarry, P. (eds) Applications of Metaheuristics in Process Engineering. Springer, Cham. https://doi.org/10.1007/978-3-319-06508-3_11

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  • DOI: https://doi.org/10.1007/978-3-319-06508-3_11

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  • Online ISBN: 978-3-319-06508-3

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