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
N1 - Publisher Copyright:
© 2014 IEEE.
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 - Banissi, Ebad
A2 - Bannatyne, Mark W. McK.
A2 - Marchese, Francis T.
A2 - Sarfraz, Muhammad
A2 - Ursyn, Anna
A2 - Venturini, Gilles
A2 - Wyeld, Theodor G.
A2 - Cvek, Urska
A2 - Trutschl, Marjan
A2 - Grinstein, Georges
A2 - Geroimenko, Vladimir
A2 - Kenderdine, Sarah
A2 - Kenderdine, Sarah
A2 - Kenderdine, Sarah
A2 - Bouali, Fatma
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 -