Paper Info
Title
X3dbio2: A Visual Analysis Tool For Biomolecular Structure Comparison
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.
Year
DOI
Venue
2013
10.1117/12.2002626
VISUALIZATION AND DATA ANALYSIS 2013
Keywords
Field
DocType
Molecular structure comparison, Molecular visualization, Interactive exploration, Protein and nucleic acids, Sequence alignment, Structure superposition, Quaternion map, Contact map, Ramachandran plot
Sequence alignment,Computer vision,Structural biology,Computer science,Biomolecular structure,Algorithm,Structural similarity,Molecular dynamics,Artificial intelligence,Ramachandran plot,Computational biology,Open source software
Conference
Volume
ISSN
Citations 
8654
0277-786X
0
PageRank 
References 
Authors
0.34
0
4
Name
Order
Citations
PageRank
hong yi100.34
Sidharth Thakur2424.28
latsavongsakda sethaphong300.34
Yaroslava G Yingling4101.42