Visual Analytics for Protein Folding

In the field of bio-informatics, the analysis of
voluminous data is becoming increasingly crucial to
understanding the underlying biology and answering
important questions. Clustering techniques often in
combination with visualization techniques are
extensively used, say, to find the functions of
unknown genes through pattern detection and analysis.
Similar to clustering of gene expression data is
that of clustering the characteristics of protein
folding dynamics. The mechanism of protein folding
remains largely a mystery. Currently, protein
folding dynamics is often characterized by
calculating the free energy landscape versus various
reaction coordinates such as the fraction of native
contacts, the radius of gyration and so on. We
present the development of a visual analytics tool,
PROTERAN, which enables one to view the changing
landscape of major protein fold states through the
metaphor of animated terrains. PROTERAN promotes the
use of an integrated approach towards understanding
the folding process via interactive visual analysis
of patterns of these reaction coordinates.

Autorentext

Kush Kapila is a Support Scientist at Accelrys Inc. in San Diego,
USA. He holds an M.Sc in Computer Science & is pursuing an MBA at
UCSD's Rady School of Management. Dr. Sudhir Mudur is Professor
in the department of Computer Science & Software Engineering at
Concordia in Montreal, CA. His research interests are 3D graphics
& virtual environments.

Klappentext

In the field of bio-informatics, the analysis of
voluminous data is becoming increasingly crucial to
understanding the underlying biology and answering
important questions. Clustering techniques often in
combination with visualization techniques are
extensively used, say, to find the functions of
unknown genes through pattern detection and analysis.
Similar to clustering of gene expression data is
that of clustering the characteristics of protein
folding dynamics. The mechanism of protein folding
remains largely a mystery. Currently, protein
folding dynamics is often characterized by
calculating the free energy landscape versus various
reaction coordinates such as the fraction of native
contacts, the radius of gyration and so on. We
present the development of a visual analytics tool,
PROTERAN, which enables one to view the changing
landscape of major protein fold states through the
metaphor of animated terrains. PROTERAN promotes the
use of an integrated approach towards understanding
the folding process via interactive visual analysis
of patterns of these reaction coordinates.