Title:	CAVER VIEWER – NEW TOOL ENHANCING COMPUTATION AND VISUALIZATION OF CHANNELS IN PROTEINS
Author(s):	Barbora Kozlíková, Ji?í Sochor, Tibor Szabó, Matúš Zamborský
ISBN:	978-972-8939-22-9
Editors:	Yingcai Xiao, Tomaz Amon and Piet Kommers
Year:	2010
Edition:	Single
Keywords:	CAVER, CAVER Viewer, visualization, protein, channel, molecular dynamics
Type:	Full Paper
First Page:	219
Last Page:	226
Language:	English
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Paper Abstract:	Protein analysis and visualization is one of the most expanding fields in the bioinformatics research. Many applications were developed till now. These programs usually concern on some specific features of proteins and provide rich functionality showing different aspects of protein structure and behavior. However, the complex tool for protein analysis, which would provide users with advanced and integrated analytic and visualization methods, is still missing. In this article, we describe the CAVER Viewer as the next tile in the mosaic of protein visualization programs. CAVER Viewer provides enhanced interface for channel analysis and a set of traditional and new techniques for visualization of the results. With the CAVER Viewer, users can explore specific paths in protein structure, which are called channels. Channels may be explored in the three-dimensional space of the molecule using the two-dimensional information and statistics, visualized as 2D graphs and connected with the 3D displaying window. In comparison to the existing applications, our program also enables working with large data sets obtained from dynamic simulations of protein behavior.
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