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A Hill-Climbing Approach for Residue Mapping in Protein Structure Alignment

  • Manish Kumar
Chapter
Part of the EAI/Springer Innovations in Communication and Computing book series (EAISICC)

Abstract

A sequence of amino acid comprises a protein structure, in which each amino acid is bounded by a peptide bond. Identifying similarity between different protein structures is known to be the most prominent research field in the current scenario. Residue mapping generally deals in identifying structural similarity in between bimolecular structures based on 3D structure. In this research work, we present a biologically inspired heuristic approach to handle the residue mapping problem in protein structure alignment. In the proposed scheme, we defined a fitness function, and based on the fitness scores, we try to find similar residues in two different protein structures. We have adopted evaluation scheme of biogeography-based optimization technique to investigate the feasibility of the presented approach over different iterations. To test the performances of the presented method, we have evaluated our methodology on real protein structure alignments and compared it with some of the well-known methods in the concerned area. The results which we gained after the experimental analysis clearly give the idea about the superiority of the presented method.

Keywords

Residue mapping Protein structure Alignment Biogeography-based optimization 

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Manish Kumar
    • 1
  1. 1.Department of Computer Science and EngineeringMadanapalle Institute of Technology and Sciences (UGC Autonomous)MadanapalleIndia

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