Abstract
AbstractWe 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.
Highlights
Recent computer graphics technology has advanced the high-resolution rendering of large-scale geometrical models with fine, smooth animation that is useful for molecular science
EPMV [1] is a new-generation molecular graphics plugin that works as an add-on tool for general-purpose 3D computer graphics (CG) animation software such as Maya (Autodesk Inc.) [2] and Blender (Blender Foundation)
Molecular dynamics simulation results can be visualized by molecular graphics programs such as UCSF Chimera [3], Cn3D [4] or BioBlender [5] using atomic coordinates
Summary
Recent computer graphics technology has advanced the high-resolution rendering of large-scale geometrical models with fine, smooth animation that is useful for molecular science. Many protein models depicted in a virtual cell Atlas could be animated to demonstrate proteinprotein interactions To accomplish this goal, we used polygon mesh models of a coarse-grained molecular surface, and displayed the dynamic conformational change of the molecules. The skeletal animation method takes advantage of recent advances in 3D CG hardware to render the shape changes of fine detailed polygon mesh models It has been used in the media industry for CG animation films and game software development. Bones can be superimposed on the polygon mesh models at arbitrary locations and with arbitrary movements This ability is useful for describing conformational changes in, and the flexibility of, protein molecules. With our results for molecular surfaces, protein ribbon models, and atomic models, we discuss possible performance improvements for the rendering of animated models using our method
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