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MoFlow: visualizing conformational changes in molecules as molecular flow improves understanding
Journal article   Open access   Peer reviewed

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

Shareef Dabdoub, R Rumpf, Amber Shindhelm and William Ray
BMC proceedings, Vol.9(Suppl 6 Proceedings of the 5th Symposium on Biological Data), pp.S5-S5
01/01/2015
DOI: 10.1186/1753-6561-9-S6-S5
PMCID: PMC4547179
PMID: 26361501
url
https://doi.org/10.1186/1753-6561-9-s6-s5View
Published (Version of record) Open Access

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. Keywords Molecular Dynamics Molecular Structural Biology Visualization Molecular Conformation

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