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Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
Published on: December 18, 2014
Visualisation of cyclic and multi-branched molecules with VMD
Simon Cross1, Michelle M Kuttel, John E Stone
1Computer Science Department, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa. hodgestar@gmail.com
Journal of Molecular Graphics & Modelling
|May 29, 2009
Summary
New visualization algorithms, PaperChain and Twister, enhance the Visual Molecular Dynamics (VMD) package for detailed analysis of complex cyclic molecules and polysaccharides. These tools offer greater flexibility in exploring molecular structures and mechanisms.
Area of Science:
- Computational chemistry
- Structural biology
- Biophysics
Background:
- Visual Molecular Dynamics (VMD) is a widely used package for molecular visualization.
- Existing VMD tools have limitations in visualizing complex cyclic and branched carbohydrate structures.
Purpose of the Study:
- To introduce two novel visualization algorithms, PaperChain and Twister, as extensions to the VMD package.
- To enhance the visualization capabilities for complex cyclic molecules, polysaccharides, and glycoconjugates.
Main Methods:
- PaperChain algorithm highlights molecular rings with colored polygons based on ring pucker.
- Twister algorithm visualizes glycosidic bonds using twisting ribbons that represent residue orientation.
- Integration of these algorithms with VMD's existing visualization features and new ring selection statements.
Main Results:
- PaperChain and Twister provide detailed visualizations of complex cyclic and multi-branched polysaccharides.
- The combined algorithms offer unprecedented flexibility in displaying various levels of detail for glycoconjugates, glycoproteins, and carbohydrate-binding proteins.
- Demonstrated efficacy in structure validation and facilitating insights into molecular structure and mechanism.
Conclusions:
- The addition of PaperChain and Twister significantly expands VMD's utility for structural analysis.
- These algorithms are valuable tools for researchers studying carbohydrate structures, glycoproteins, and related molecular mechanisms.
- Enhanced visualization aids in understanding complex molecular architectures and their functional implications.
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