X3DBio2: A visual analysis tool for biomolecular structure comparison

Hong Yi; Sidharth Thakur; Latsavongsakda Sethaphong; Yaroslava G. Yingling

doi:10.1117/12.2002626

4 February 2013 X3DBio2: A visual analysis tool for biomolecular structure comparison

Hong Yi, Sidharth Thakur, Latsavongsakda Sethaphong, Yaroslava G. Yingling

Proceedings Volume 8654, Visualization and Data Analysis 2013; 86540W (2013) https://doi.org/10.1117/12.2002626
Event: IS&T/SPIE Electronic Imaging, 2013, Burlingame, California, United States

Abstract

A major problem in structural biology is the recognition of differences and similarities between related three dimensional (3D) biomolecular structures. Investigating these structure relationships is important not only for understanding of functional properties of biologically significant molecules, but also for development of new and improved materials based on naturally-occurring molecules. We developed a new visual analysis tool, X3DBio2, for 3D biomolecular structure comparison and analysis. The tool is designed for elucidation of structural effects of mutations in proteins and nucleic acids and for assessment of time dependent trajectories from molecular dynamics simulations. X3DBio2 is a freely downloadable open source software and provides tightly integrated features to perform many standard analysis and visual exploration tasks. We expect this tool can be applied to solve a variety of biological problems and illustrate the use of the tool on the example study of the differences and similarities between two proteins of the glycosyltransferase family 2 that synthesize polysaccharides oligomers. The size and conformational distances and retained core structural similarity of proteins SpsA to K4CP represent significant epochs in the evolution of inverting glycosyltransferases.

Citation Download Citation

Hong Yi, Sidharth Thakur, Latsavongsakda Sethaphong, and Yaroslava G. Yingling "X3DBio2: A visual analysis tool for biomolecular structure comparison", Proc. SPIE 8654, Visualization and Data Analysis 2013, 86540W (4 February 2013); https://doi.org/10.1117/12.2002626

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