If you are looking at 2D, schematic diagrams like the following figure: You can use My Domains.
Similar schematic diagrams can be generated from protein structure (seee the following figure) data using DOMPLOT.
If you are looking at 3D structure visualization of your gene/protein: Try one of the following tools:
- PyMol: Educational use is free,
- Molscript / Raster3D: Very
powerful visualization programs,
- Jmol: Web based, Java applet
- Several other tools are available here and here
See an example MolScript figure below:
If you like coding, you could also give TiKZ a try: http://www.texample.net/tikz/examples/area/biology/
TiKZ has a steep learning curve, but once you get the hold of it, making nice illustrations become really fun.
You can use the newly released lollipop tool from cBioPortal team. Just modify input to include header and gene name for protein of interest:
The resultant protein diagram can be edited in SVG editor to remove extraneous graphical elements.
Tool can be founder here: