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International Workshop on DNA-Based Computers

DNA 2004: DNA Computing pp 308–318Cite as

Toward “Wet” Implementation of Genetic Algorithm for Protein Engineering

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Part of the Lecture Notes in Computer Science book series (LNTCS,volume 3384)

Abstract

We here propose an application of DNA computing to a practical problem, protein engineering, which is difficult to approach by using modern electronic computers. DNA molecules naturally carry the blueprints of proteins. DNA-based processing of this genetic information could give mutant proteins with desired properties. We conceived the use of genetic algorithm for this purpose, and designed an algorithm amenable to DNA-based implementation. The performance of this algorithm was examined on a model fitness landscape by computer experiments. Then, spontaneous DNA recombination during PCR was utilized to embody the crossover operation in the genetic algorithm, preparing for the “wet” implementation of the whole search process in the future.

Keywords

  • Genetic Algorithm
  • Search Generation
  • Protein Engineer
  • Modern Electronic Computer
  • Crossover Site

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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  • DOI: 10.1007/11493785_27
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Author information

Authors and Affiliations

  1. Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033

    Kensaku Sakamoto

  2. RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan

    Kensaku Sakamoto

  3. Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama, 226-0026, Japan

    Masayuki Yamamura

  4. Department of Prediction and Control, The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minato-ku, Tokyo, 106-8569, Japan

    Hiroshi Someya

Authors
  1. Kensaku Sakamoto
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  2. Masayuki Yamamura
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  3. Hiroshi Someya
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Editor information

Editors and Affiliations

  1. Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano – Bicocca, Via Bicocca degli Arcimboldi 8, 20126, Milano, Italy

    Claudio Ferretti & Claudio Zandron & 

  2. Complex Systems and Artificial Intelligence Research Center, University of Milan–Bicocca, Italy

    Giancarlo Mauri

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© 2005 Springer-Verlag Berlin Heidelberg

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Sakamoto, K., Yamamura, M., Someya, H. (2005). Toward “Wet” Implementation of Genetic Algorithm for Protein Engineering. In: Ferretti, C., Mauri, G., Zandron, C. (eds) DNA Computing. DNA 2004. Lecture Notes in Computer Science, vol 3384. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11493785_27

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  • DOI: https://doi.org/10.1007/11493785_27

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-26174-2

  • Online ISBN: 978-3-540-31844-6

  • eBook Packages: Computer ScienceComputer Science (R0)