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Updated: May 18, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
NetworkView: 3D display and analysis of protein·RNA interaction networks
John Eargle1, Zaida Luthey-Schulten
1Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue Urbana, IL 61801, USA.
Bioinformatics (Oxford, England)
|September 18, 2012
Summary
NetworkView is a VMD plugin for visualizing and analyzing protein-RNA interaction networks. It links network data to 3D molecular structures for integrated analysis.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Protein-RNA interactions are crucial for cellular function.
- Analyzing these interactions requires specialized tools for complex network data.
Purpose of the Study:
- To introduce NetworkView, a novel application for visualizing and analyzing protein-RNA interaction networks.
- To couple network analysis with underlying 3D molecular structures.
Main Methods:
- NetworkView models protein residues and nucleic acid monomers as nodes, with pairwise contacts as weighted edges.
- The application projects interaction networks onto 3D molecular structures.
- NetworkView is implemented as a plugin for the VMD molecular visualization software.
Main Results:
- Enables the display and analysis of protein-RNA interaction networks.
- Facilitates the integration of network properties with physical and biological characteristics of molecules.
- Provides a user-friendly interface within VMD for complex network visualization.
Conclusions:
- NetworkView enhances the study of protein-RNA interactions by integrating network analysis with 3D structural data.
- The tool aids in understanding the physical and biological implications of these interactions.
- NetworkView is readily available as a VMD plugin, promoting its adoption in structural biology research.
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