Intuitive helix representation and geometry analysis

Bendix is a user-friendly, multi-platform and free plugin for VMD, that makes it easier to characterize proteins. It allows you to calculate and visualize both dynamic and static helix geometry, and abstracts helices without sacrificing conformation. Moreover it accepts both coarse-grained and atomistic proteins.

Bendix displays protein helices as cylinders that follow the helix axis. This captures conformational information that is lost if you use classical, straight cylinders. Coarse-grained proteins also benefit from beta-sheet and backbone display. Helix geometry can be analysed both qualitatively, using the revealing heatmap colour-coding, and quantitatively, where data is 2D or 3D graphed, with the option to export for viewing with common graphing packages. With its multiple settings, Bendix is easily tailored.

Bendix integrates with the rest of VMD, so there is nothing stopping you from using Bendix in addition to, say, Graphical Representations. For Bendix examples and screenshots, please view the slideshows and the Gallery and Tutorial sections of the Bendix home page.

If you use Bendix for a publication, please cite it!

Dahl ACE, Chavent M and Sansom MSP (2012) Bendix: intuitive helix geometry analysis and abstraction. Bioinformatics 28 (16): 2193-2194.