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Updated: Jun 12, 2026
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Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations
Aleksey Porollo1, Jaroslaw Meller
1Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA. alexey.porollo@uc.edu
Nucleic Acids Research
|May 28, 2010
Summary
POLYVIEW-MM integrates molecular motion animation with structural analysis for macromolecules. This tool aids in interpreting simulation data by visualizing conformational changes and functional sites.
Area of Science:
- Structural biology
- Computational biology
- Biophysics
Background:
- Molecular simulations provide insights into macromolecular mechanisms and functions.
- Interpreting simulation data requires integrated tools for structural databases and web resources.
Purpose of the Study:
- To present POLYVIEW-MM, a novel web server for animating molecular motion and analyzing macromolecular structures.
- To enhance the interpretation of molecular dynamics and related simulation techniques.
Main Methods:
- Animation of molecular dynamics trajectories and visualization of alternative conformers.
- Integration of Jmol for interactive conformational analysis and PyMol for publication-quality animation.
- Customizable 2D plots for summarizing molecular motion, secondary structure, and solvent accessibility.
Main Results:
- POLYVIEW-MM enables high-quality animation of molecular motion (MM).
- The server visualizes conformational changes and integrates structural annotations like interaction sites, binding pockets, and domains.
- It provides interactive analysis of macromolecular structures and simulation data.
Conclusions:
- POLYVIEW-MM offers a versatile platform for analyzing macromolecular simulations.
- The tool facilitates a deeper understanding of protein dynamics and function through integrated visualization and analysis.
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