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 |
| Publisher | Institute of Electrical and Electronics Engineers Inc. |
| Pages | 164-169 |
| Number of pages | 6 |
| ISBN (Electronic) | 9781479941032 |
| DOIs | |
| 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 |
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 |
Fingerprint
Keywords
- Amino acid
- Pocket identification
- Protein
- Visualization
ASJC Scopus subject areas
- Computer Science(all)
- Engineering(all)
Cite this
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. Institute of Electrical and Electronics Engineers Inc., 2014. p. 164-169 6902898.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
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
SP - 164
EP - 169
BT - Proceedings - 2014 18th International Conference on Information Visualisation
PB - Institute of Electrical and Electronics Engineers Inc.
ER -