A visual analytics of geometric distances between amino acids and surface pockets of proteins

Makiko Miyoshi, Ayaka Kaneko, Takayuki Itoh, Kei Yura

研究成果: Conference contribution

1 被引用数 (Scopus)

抄録

Protein is the major component of the organism. It has a unique three-dimensional structure determined by its amino acid sequence. A concave (pocket) on the surface of a protein is known to be the best target for a drug to react. We started analyzing how' drug ability' of proteins related to the location of amino acids in a pocket. For as tarter of the study, this paper presents a visualization tool for distance analysis between pockets and the amino acid residue. Provided that a protein surface is described by a triangular mesh, this tool first identifies pockets on the protein surface, specifies the deepest point and outer loops of the pocket, and calculates distances between atoms of an amino acid residue and the deepest point or the outer loops of the pocket. The tool then visualizes the statistics of the distance calculation results by poly line charts and the distribution by scatter plots. This paper proposes a biological interpretation of the visualization results.

本文言語English
ホスト出版物のタイトルProceedings - 2014 18th International Conference on Information Visualisation
ホスト出版物のサブタイトルVisualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014
編集者Francis T. Marchese, Urska Cvek, Marjan Trutschl, Georges Grinstein, Anna Ursyn, Gilles Venturini, Theodor G. Wyeld, Sarah Kenderdine, Fatma Bouali, Muhammad Sarfraz, Ebad Banissi, Mark W. McK. Bannatyne, Vladimir Geroimenko, Sarah Kenderdine, Sarah Kenderdine
出版社Institute of Electrical and Electronics Engineers Inc.
ページ164-169
ページ数6
ISBN(電子版)9781479941032
DOI
出版ステータスPublished - 2014 9 18
外部発表はい
イベント2014 18th International Conference on Information Visualisation: Visualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014 - Paris, France
継続期間: 2014 7 162014 7 18

出版物シリーズ

名前Proceedings of the International Conference on Information Visualisation
ISSN(印刷版)1093-9547

Other

Other2014 18th International Conference on Information Visualisation: Visualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014
国/地域France
CityParis
Period14/7/1614/7/18

ASJC Scopus subject areas

  • ソフトウェア
  • 信号処理
  • コンピュータ ビジョンおよびパターン認識

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