HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures
2008
HOLLOW: A Program for Visualizing Protein Channel Surfaces
publication
Evidence: moderate
Author Information
Author(s): Ho Bosco, Gruswitz Franz
Primary Institution: University of California, San Francisco
Hypothesis
Can a program be developed to accurately visualize the interior surfaces of protein channels?
Conclusion
HOLLOW simplifies the generation of channel surfaces and other interior surfaces of protein structures.
Supporting Evidence
- HOLLOW generates a PDB file of dummy atoms that closely approximates the channel surface.
- The program allows for customization of surface rendering, improving visualization clarity.
- Dummy atoms can be used to select channel residues by proximity.
Takeaway
HOLLOW is a tool that helps scientists see the insides of protein channels more clearly, making it easier to understand how they work.
Methodology
HOLLOW uses dummy atoms to fill the empty space inside a protein structure, allowing for clean visualizations of channel surfaces.
Limitations
The accuracy of the visualization can depend on grid spacing, and higher accuracy requires more computation time.
Digital Object Identifier (DOI)
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