MoFlow: Visualizing conformational changes in molecules as molecular flow improves understanding

Abstract

Background: Current visualizations of molecular motion use a Timeline-analogous representation that conveys first the molecule was shaped like this, then like this.. This scheme is orthogonal to the Pathline-like human understanding of motion this part of the molecule moved from here to here along this path. We present MoFlow, a system for visualizing molecular motion using a Pathline-analogous representation. Results: The MoFlow system produces high-quality renderings of molecular motion as atom pathlines, as well as interactive WebGL visualizations, and 3D printable models. In a preliminary user study, MoFlow representations are shown to be superior to canonical representations for conveying molecular motion. Conclusions: Pathline-based representations of molecular motion are more easily understood than timeline representations. Pathline representations provide other advantages because they represent motion directly, rather than representing structure with inferred motion.