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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Visualizing protein conformational changes on a personal computer--alpha carbon pseudo bonding as a constraint for
1School of Biochemistry & Molecular Biology and Flexible Learning Development Unit, University of Leeds, Leeds LS2 9JT, UK. a.g.booth@leeds.ac.uk
Journal of Molecular Graphics & Modelling
|September 13, 2001
Summary
This study introduces a Java program for creating protein conformation change animations. The software visualizes interpolated protein structures, aiding in understanding molecular dynamics for educational purposes.
Area of Science:
- Biochemistry
- Computational Biology
- Structural Biology
Background:
- Understanding protein conformational changes is crucial for molecular biology and drug discovery.
- Visualizing these dynamic processes aids in education and research.
Purpose of the Study:
- To develop a user-friendly Java program for generating animations of protein conformational changes.
- To create a tool for visualizing interpolated protein structures for teaching and research.
Main Methods:
- Developed a Java program to visualize a series of aligned protein structures.
- Interpolated intermediate protein structures in internal coordinate space.
- Introduced 'pseudo' bonds between alpha carbon atoms to constrain backbone movements and prevent artifacts.
Main Results:
- Successfully generated animations and movies (AVI format) of protein conformation changes.
- The program produces plausible intermediate structures by interpolating between two known protein forms.
- All steps, including alignment and movie production, are feasible on personal computers.
Conclusions:
- The developed Java program provides an accessible tool for visualizing protein dynamics.
- This method facilitates the creation of educational materials on protein conformational changes.
- The approach offers a practical way to study molecular movements on standard hardware.
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