Skeletal animation for visualizing dynamic shapes of macromolecules

Abstract

We apply a skeletal animation technique developed for general computer graphics animation to display the dynamic shape of protein molecules. Polygon-based models for macromolecules such as atomic representations, surface models, and protein ribbon models are deformed by the motion of skeletal bones that provide coarse-grained descriptions of detailed computer graphics models. Using the animation software Blender, we developed methods to generate the skeletal bones for molecules. Our example of the superposition of normal modes demonstrates the thermal fluctuating motion obtained from normal mode analysis. The method is also applied to display the motions of protein molecules using trajectory coordinates of a molecular dynamics simulation. We found that a standard motion capture file was practical and useful for describing the motion of the molecule using available computer graphics tools.

Keywords

• molecular dynamics
• molecular visualization
• normal mode analysis
• structure of protein molecule