Techniques for visualization of carbohydrate molecules.
Standard molecular visualizations, such as the classic ball-and-stick model, are not suitable for large, complex molecules because the overall molecular structure is obscured by the atomic detail. For proteins, the more abstract ribbon and cartoon representations are instead used to reveal large scale molecular conformation and connectivity. However, there is currently no accepted convention for simplifying oligo- and polysaccharide structures. We introduce two novel visualization algorithms for carbohydrates, incorporated into a visualization package, CarboHydra. Both algorithms highlight the sugar rings and backbone conformation of the carbohydrate chain, ignoring ring substituents. The first algorithm, termed PaperChain, emphasizes the type and conformation of the carbohydrate rings. The second, Twister, emphasizes the relative orientation of the rings. We further include two rendering enhancements to augment these visualizations: silhouettes edges and a translucent overlay of the ball-and-stick atomic representation. To demonstrate their utility, the algorithms and visualization enhancements are here applied to a variety of carbohydrate molecules. User evaluations indicate that they present a more useful view of carbohydrate structure than the standard ball-and-stick representation. The algorithms were found to be complementary, with PaperChain particularly effective for smaller carbohydrates and Twister useful at larger scales for highlighting the backbone twist of polysaccharides.
Collaborative Visual Computing Laboratory, Computer Science Department, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa. mkuttel@cs.uct.ac.za
Michelle
M
Kuttel
James
J
Gain
Anton
A
Burger
Ian
I
Eborn
D000465:Algorithms; D002236:Carbohydrate Conformation; D002241:Carbohydrates / Q000737:chemistry*; D003196:Computer Graphics; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D021621:Imaging, Three-Dimensional; D008958:Models, Molecular
D002241:Carbohydrates; D004247:DNA