Distance Distribution Analysis in Pockets among Amino Acids

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  • 蛋白質ポケットとアミノ酸間の距離分布分析(ポスター(生活支援・アート・可視化),映像表現・芸術科学フォーラム2013)
  • 蛋白質ポケットとアミノ酸間の距離分布分析
  • タンパクシツ ポケット ト アミノサン カン ノ キョリ ブンプ ブンセキ

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Abstract

Protein is the major component of the organism. It has a unique typical three-dimensional structure determined by the sequence of, amino acids. A hole (pocket) on the surface of a protein is known to be the best target for a drug to react. We started analyzing how "druggability" of proteins related to the locations amino acids in a pocket. For a starter of this study, this paper presents a visualization tool for distance distribution analysis between two types of amino acids in a pocket. When protein surface is provided by triangular meshes, this tool first identifies a pocket from the protein surface, specifies the deepest position of the pockets, and calculates distances between atoms of an amino acid and the deepest positions of the pocket. This tool then visualizes the distribution of the distances by scatterplots. This paper proposes the a biological interpretation of the visualization results.

Journal

  • ITE Technical Report

    ITE Technical Report 37.17 (0), 243-246, 2013

    The Institute of Image Information and Television Engineers

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