FTDock (v2.0)
(Fourier Transform rigid-body Docking)The FTDock algorithm is based on that of Katchalski-Katzir. It discretises the two molecules onto orthogonal grids and performs a global scan of translational and rotational space. In order to scan rotational space it is necessary to rediscretise one of the molecules (for speed the smaller) for each rotation. The scoring method is primarily a surface complementarity score between the two grids. To speed up the surface complementarity calculations, which are convolutions of two grids, Fourier Transforms are used. This means that the convolutions are replaced with multiplications in Fourier space, and despite having to perform the forward and reverse Fourier Transforms, this decreases the overall computation required. The surface complementarity was the only score used in the original method. The original work on FTDock (Gabb et.al. 1997) found it a useful addition to include an electrostatic filter, and this is again implemented in the current version (though it can be turned off).
For a fuller description of the algorithm, installation instructions, a step by step tutorial, and program manual, please see the 3D-Dock Manual (PDF).
You will need to compile FFTW prior to compiling FTDock. A local copy is available.