Prediction of protein inter-domain linkers using compositional index and simulated annealing

Maad Shatnawi, Nazar Zaki

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

6 Citations (Scopus)

Abstract

Protein chains are typically large and consist of multiple domains which are difficult and computationally expensive to characterize using experimental methods. Therefore, accurate and reliable prediction of protein domain boundaries is often the initial step in both experimental and computational protein research. In this paper, we propose a straightforward yet effective method to predict inter-domain linker segments by using the amino acid compositional index from the amino acid sequence information. Each amino acid in the protein sequence is represented by a compositional index which is deduced from a combination of the difference in amino acid occurrences in domains and linker segments in training protein sequences and the amino acid composition information. Further, we employ simulated annealing to improve the prediction by finding the optimal set of threshold values that separate domains from inter-domain linkers. The performance of the proposed method is compared to the current approaches on two protein sequence datasets. Experimental results show superior performance by the proposed method when compared to the state-of-the-art methods for inter-domain linker prediction.

Original languageEnglish
Title of host publicationGECCO 2013 - Proceedings of the 2013 Genetic and Evolutionary Computation Conference Companion
Pages1603-1608
Number of pages6
DOIs
Publication statusPublished - 2013
Event15th Annual Conference on Genetic and Evolutionary Computation, GECCO 2013 - Amsterdam, Netherlands
Duration: Jul 6 2013Jul 10 2013

Publication series

NameGECCO 2013 - Proceedings of the 2013 Genetic and Evolutionary Computation Conference Companion

Other

Other15th Annual Conference on Genetic and Evolutionary Computation, GECCO 2013
Country/TerritoryNetherlands
CityAmsterdam
Period7/6/137/10/13

Keywords

  • Amino acid composition
  • Compositional index
  • Domain boundary prediction
  • Domain linkers
  • Inter-domain linker segments
  • Protein sequences
  • Simulated annealing

ASJC Scopus subject areas

  • Computational Mathematics

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