Visual Analytics for Protein Folding: PROTERAN: Analyzing Protein Folds Using Animated Terrains

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.

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.