Intuitive helix representation and geometry analysis
Bendix is a user-friendly, multi-platform and free plugin for Visual Molecular Dynamics (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 slideshow above, and see the Gallery and Tutorial sections of this website.
Helix dynamics is important
Alpha helix flexibility plays a key role in the mechanisms of gating of ion channels and solute transporters. Examples of this can be seen in the voltage-gated potassium channel, KcsA, and the mechanosensitive channel of small conductance, MscS, where molecular hinges within channel-lining helices are important for gating. KscA and MscS are not exceptional - membrane proteins often feature curved or kinked helices, and dynamics of many such "non-ideal" helices is critical to protein function. However, non-linear helices are compromised by current visualization techniques, and call for better characterization. Bendix was developed to meet these demands.
Visualising coarse-grained proteins
Coarse-graining (CG) joins adjacent atoms into larger 'functional group particles', thereby reducing the number of particles in your system. Fewer particles mean that fewer inter-particle interactions need to be calculated, which speeds up computation and can allow physiologically relevant simulation time-scales. However, amazingly long trajectories are no good if you can't see them, and up until now, CG visualization was very sparse. Bendix incorporates CG secondary structure representation, making it possible to view the time evolution of physiological events at the molecular level, at a useful level of abstraction.
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.