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

Makiko Miyoshi; Ayaka Kaneko; Takayuki Itoh; Kei Yura

doi:10.1109/IV.2014.38

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 proceeding › Conference 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 language	English
Title of host publication	Proceedings - 2014 18th International Conference on Information Visualisation
Subtitle of host publication	Visualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014
Editors	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
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	164-169
Number of pages	6
ISBN (Electronic)	9781479941032
DOIs	https://doi.org/10.1109/IV.2014.38
Publication status	Published - 2014 Sep 18
Externally published	Yes
Event	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 Duration: 2014 Jul 16 → 2014 Jul 18

Publication series

Name	Proceedings of the International Conference on Information Visualisation
ISSN (Print)	1093-9547

Other

Other	2014 18th International Conference on Information Visualisation: Visualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014
Country	France
City	Paris
Period	14/7/16 → 14/7/18

Keywords

Amino acid
Pocket identification
Protein
Visualization

ASJC Scopus subject areas

Software
Signal Processing
Computer Vision and Pattern Recognition

Access to Document

10.1109/IV.2014.38

Fingerprint Dive into the research topics of 'A visual analytics of geometric distances between amino acids and surface pockets of proteins'. Together they form a unique fingerprint.

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

A visual analytics of geometric distances between amino acids and surface pockets of proteins. / Miyoshi, Makiko; Kaneko, Ayaka; Itoh, Takayuki; Yura, Kei.

Proceedings - 2014 18th International Conference on Information Visualisation: Visualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014. ed. / 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. Institute of Electrical and Electronics Engineers Inc., 2014. p. 164-169 6902898 (Proceedings of the International Conference on Information Visualisation).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Miyoshi, M, Kaneko, A, Itoh, T & Yura, K 2014, A visual analytics of geometric distances between amino acids and surface pockets of proteins. in FT Marchese, U Cvek, M Trutschl, G Grinstein, A Ursyn, G Venturini, TG Wyeld, S Kenderdine, F Bouali, M Sarfraz, E Banissi, MWM 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., 6902898, Proceedings of the International Conference on Information Visualisation, Institute of Electrical and Electronics Engineers Inc., pp. 164-169, 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, 14/7/16. https://doi.org/10.1109/IV.2014.38

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

Miyoshi, Makiko ; Kaneko, Ayaka ; Itoh, Takayuki ; Yura, Kei. / A visual analytics of geometric distances between amino acids and surface pockets of proteins. Proceedings - 2014 18th International Conference on Information Visualisation: Visualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014. editor / 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. Institute of Electrical and Electronics Engineers Inc., 2014. pp. 164-169 (Proceedings of the International Conference on Information Visualisation).

@inproceedings{0fbbd546ddc443c099853c88cc7185e0,

title = "A visual analytics of geometric distances between amino acids and surface pockets of proteins",

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.",

keywords = "Amino acid, Pocket identification, Protein, Visualization",

author = "Makiko Miyoshi and Ayaka Kaneko and Takayuki Itoh and Kei Yura",

year = "2014",

month = sep,

day = "18",

doi = "10.1109/IV.2014.38",

language = "English",

series = "Proceedings of the International Conference on Information Visualisation",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "164--169",

editor = "Marchese, {Francis T.} and Urska Cvek and Marjan Trutschl and Georges Grinstein and Anna Ursyn and Gilles Venturini and Wyeld, {Theodor G.} and Sarah Kenderdine and Fatma Bouali and Muhammad Sarfraz and Ebad Banissi and Bannatyne, {Mark W. McK.} and Vladimir Geroimenko and Sarah Kenderdine and Sarah Kenderdine",

booktitle = "Proceedings - 2014 18th International Conference on Information Visualisation",

note = "2014 18th International Conference on Information Visualisation: Visualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014 ; Conference date: 16-07-2014 Through 18-07-2014",

}

TY - GEN

T1 - A visual analytics of geometric distances between amino acids and surface pockets of proteins

AU - Miyoshi, Makiko

AU - Kaneko, Ayaka

AU - Itoh, Takayuki

AU - Yura, Kei

PY - 2014/9/18

Y1 - 2014/9/18

N2 - 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.

AB - 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.

KW - Amino acid

KW - Pocket identification

KW - Protein

KW - Visualization

UR - http://www.scopus.com/inward/record.url?scp=84912101642&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84912101642&partnerID=8YFLogxK

U2 - 10.1109/IV.2014.38

DO - 10.1109/IV.2014.38

M3 - Conference contribution

AN - SCOPUS:84912101642

T3 - Proceedings of the International Conference on Information Visualisation

SP - 164

EP - 169

BT - Proceedings - 2014 18th International Conference on Information Visualisation

A2 - Marchese, Francis T.

A2 - Cvek, Urska

A2 - Trutschl, Marjan

A2 - Grinstein, Georges

A2 - Ursyn, Anna

A2 - Venturini, Gilles

A2 - Wyeld, Theodor G.

A2 - Kenderdine, Sarah

A2 - Bouali, Fatma

A2 - Sarfraz, Muhammad

A2 - Banissi, Ebad

A2 - Bannatyne, Mark W. McK.

A2 - Geroimenko, Vladimir

A2 - Kenderdine, Sarah

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2014 18th International Conference on Information Visualisation: Visualisation, BioMedical Visualization, Visualisation on Built and Rural Environments and Geometric Modelling and Imaging, IV 2014

Y2 - 16 July 2014 through 18 July 2014

ER -