Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Techniques for visualization of carbohydrate molecules.

Michelle Kuttel1, James Gain, Anton Burger

  • 1Collaborative Visual Computing Laboratory, Computer Science Department, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa. mkuttel@cs.uct.ac.za

Journal of Molecular Graphics & Modelling
|March 28, 2006
PubMed
Summary

New visualization algorithms, PaperChain and Twister, simplify complex carbohydrate structures. These methods improve the understanding of oligosaccharide and polysaccharide conformations, overcoming limitations of traditional molecular models.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The physiological signature of sadness: A comparison between text, film and virtual reality.

Brain and cognition·2021
Same author

Visual Computing and the Progress of Developing Countries.

IEEE computer graphics and applications·2016
Same author

Simulation of Coarse-Grained Protein-Protein Interactions with Graphics Processing Units.

Journal of chemical theory and computation·2015
Same author

Comparative simulation of pneumococcal serogroup 19 polysaccharide repeating units with two carbohydrate force fields.

Carbohydrate research·2014
Same author

Moving least-squares reconstruction of large models with GPUs.

IEEE transactions on visualization and computer graphics·2013
Same author

Efficient compression of molecular dynamics trajectory files.

Journal of computational chemistry·2012

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • Traditional molecular visualizations like ball-and-stick models obscure complex structures.
  • Protein visualization uses abstract methods (ribbon, cartoon) for large-scale conformation.
  • No standardized visualization convention exists for oligo- and polysaccharides.

Purpose of the Study:

  • Introduce novel visualization algorithms for carbohydrates.
  • Develop a visualization package, CarboHydra, for enhanced carbohydrate representation.
  • Address the lack of accepted conventions in carbohydrate structural visualization.

Main Methods:

  • Developed two novel algorithms: PaperChain and Twister.
  • Implemented algorithms within the CarboHydra visualization package.

Related Experiment Videos

  • Incorporated rendering enhancements: silhouette edges and translucent ball-and-stick overlays.

    • Main Results:

    • Algorithms highlight sugar rings and backbone conformation, omitting substituents.
    • PaperChain emphasizes ring type and conformation; Twister emphasizes relative ring orientation.
    • User evaluations show improved utility over standard ball-and-stick representations.

    Conclusions:

    • PaperChain is effective for smaller carbohydrates; Twister excels with larger polysaccharides.
    • The novel algorithms and enhancements provide a more useful view of carbohydrate structure.
    • These tools offer complementary approaches for visualizing complex carbohydrate molecules.