MEMSAT-SVM - Predict transmembrane protein topology using support vector machines.
MEMSAT-SVM-PORE - Predict pore-lining residues and helices in transmembrane proteins (beta).
MEMPACK - Predict residue-residue contacts and helix packing in transmembrane proteins.
FILM3 - De novo 3D structure prediction of transmembrane proteins.
Below are a couple of Perl modules for drawing cartoons and schematics of alpha-helical transmembrane proteins. Each contains documentation within the module (do 'perldoc DrawTransmembrane' or 'perldoc DrawTransmembraneSchematic') and test scripts. DrawTransmembrane.pm is also available as part of BioPerl. These all require the GD module, and DrawHelicalWheel requires GD::SVG for scalable vector graphics. Please let me know if you find any bugs.
Use this to draw and label cartoons of alpha-helical transmembrane proteins:
Use this to draw a schematic showing multiple topologies, construct a Kyte-Doolittle hydropathy plot and to generate a consensus:
Use this to draw a wheel representation of an alpha-helix. Useful for spotting amphipathic and pore forming helices. Can output to SVG (this image converted to PNG):