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3D Protein Peptide Chain Search Using an Improved Genetic Algorithm

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Book cover Computational Science and Its Applications — ICCSA 2003 (ICCSA 2003)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2667))

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Abstract

In this paper, an efficient searching algorithm, namely intergeneration projection micro genetic algorithm (IP-μGA) is introduced to search the three dimensional protein conformations. A bond rotation model is developed, in which variables are the dihedral angles along peptide main chain. The root mean square deviation (RMSD) is adopted as the fitness function in the searching process and the template protein structures in protein data bank (PDB) are used for comparison. The results of 3D peptide structures of examples show the effectiveness of present method.

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Author information

Authors and Affiliations

  1. Center for Advanced Computations in Engineering Science (ACES), Department of Mechanical Engineering, National University of Singapore, Singapore, 119260

    Zhenglin Yang & Guirong Liu

Authors
  1. Zhenglin Yang
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  2. Guirong Liu
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Editor information

Editors and Affiliations

  1. Army High Performance Computing Research Center, USA

    Vipin Kumar

  2. Department of Computer Science, University of Calgary, Calgary, AB, T2N1N4, Canada

    Marina L. Gavrilova

  3. Heuchera Technologies Inc., 122 9251-8 Yonge Street, Richmond Hill, ON, Canada, L4C 9T3

    Chih Jeng Kenneth Tan

  4. Département d’informatique et de recherche opérationelle, Université de Montréal, Montréal, Québec, H3C 3J7, Canada

    Pierre L’Ecuyer

  5. Department of Computer Science and Engineering, University of Minessota, MN, 55455, USA

    Vipin Kumar

  6. The Queen’s University of Belfast, School of Computer Science, Belfast BT7 1NN, Northern Ireland, UK

    Chih Jeng Kenneth Tan

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© 2003 Springer-Verlag Berlin Heidelberg

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Yang, Z., Liu, G. (2003). 3D Protein Peptide Chain Search Using an Improved Genetic Algorithm. In: Kumar, V., Gavrilova, M.L., Tan, C.J.K., L’Ecuyer, P. (eds) Computational Science and Its Applications — ICCSA 2003. ICCSA 2003. Lecture Notes in Computer Science, vol 2667. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44839-X_35

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  • DOI: https://doi.org/10.1007/3-540-44839-X_35

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-40155-1

  • Online ISBN: 978-3-540-44839-6

  • eBook Packages: Springer Book Archive

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