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

Makiko Miyoshi, Ayaka Kaneko, Takayuki Itoh, Kei Yura

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

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationProceedings - 2014 18th International Conference on Information Visualisation
Subtitle of host publicationVisualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014
EditorsFrancis 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
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages164-169
Number of pages6
ISBN (Electronic)9781479941032
DOIs
Publication statusPublished - 2014 Sep 18
Externally publishedYes
Event2014 18th International Conference on Information Visualisation: Visualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014 - Paris, France
Duration: 2014 Jul 162014 Jul 18

Publication series

NameProceedings of the International Conference on Information Visualisation
ISSN (Print)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
CountryFrance
CityParis
Period14/7/1614/7/18

Keywords

  • Amino acid
  • Pocket identification
  • Protein
  • Visualization

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Computer Vision and Pattern Recognition

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  • Cite this

    Miyoshi, M., Kaneko, A., Itoh, T., & Yura, K. (2014). A visual analytics of geometric distances between amino acids and surface pockets of proteins. In F. T. Marchese, U. Cvek, M. Trutschl, G. Grinstein, A. Ursyn, G. Venturini, T. G. Wyeld, S. Kenderdine, F. Bouali, M. Sarfraz, E. Banissi, M. W. M. Bannatyne, V. Geroimenko, S. Kenderdine, & S. Kenderdine (Eds.), Proceedings - 2014 18th International Conference on Information Visualisation: Visualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014 (pp. 164-169). [6902898] (Proceedings of the International Conference on Information Visualisation). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/IV.2014.38