A novel clustering based niching EDA for protein folding

Benhui Chen, Jinglu Hu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

Protein structure prediction (PSP) is one of the most important problems in computational biology. And it also is a very difficult optimization task, especially for long sequence instances. This paper proposes a novel clustering based niching EDA for HP model folding problem. The EDA individuals are clustered by the affinity propagation clustering method before submitting them to niching clearing. A cluster can be seen as a niche in clearing procedure. The niche clearing radius can be adaptively determined by clustering. And an approach based on Boltzmann scheme is proposed to determine the niche capacity according to the adaptive clearing radius and niche fitness. Experimental results demonstrate that the proposed method outperforms the basic EDAs method. At the same time, it is very competitive with other existing algorithms for the PSP problem on lattice HP models.

Original languageEnglish
Title of host publication2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Proceedings
Pages748-753
Number of pages6
DOIs
Publication statusPublished - 2009 Dec 1
Event2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Coimbatore, India
Duration: 2009 Dec 92009 Dec 11

Publication series

Name2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Proceedings

Conference

Conference2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009
CountryIndia
CityCoimbatore
Period09/12/909/12/11

ASJC Scopus subject areas

  • Artificial Intelligence
  • Computer Science Applications
  • Software

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  • Cite this

    Chen, B., & Hu, J. (2009). A novel clustering based niching EDA for protein folding. In 2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Proceedings (pp. 748-753). [5393870] (2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Proceedings). https://doi.org/10.1109/NABIC.2009.5393870