Cell-Dock: high-performance protein-protein docking

Carles Pons, Daniel Jimenez-Gonzalez, Cecilia Gonzalez-Alvarez, Harald Servat, Daniel Cabrera-Benitez, Xavier Aguilar, Juan Fernandez-Recio

In this work we present a new FFT-based docking method optimized for the Cell BE processor. For the sake of efficiency, Cell-Dock forces the grid size to be a power of 2, making the grid resolution variable. To validate this atypical approach, we have run tests using the protein-protein docking benchmark [Mintseris et al, Proteins 2005], and thoroughly compared the results with those of FTDock [Gabb et al, J Mol Biol 1997]. Results show that Cell-Dock runs faster (with speedups up to 226.5 depending on the version) and achieves results of similar quality. The program also runs on PlayStation 3. The source code is released under GNU General Public License version 2.

This software comes with absolutely no warranty.
Please, read carefully the license before downloading the program.

Download Cell-Dock (source code) (license and examples are included)

Compilation instructions:
  • The compilation requires the IBM FFT libraries that are part of the SDK. If needed, they can be downloaded here
  • Modify SDK path and MPI path in the Makefile of the root directory
  • Run make in the libs-cell folder
  • Run make in the progs-cell folder


Speedups between the different versions of Cell-Dock (with 128 and 256 grid size) and FTDock (using 0.7 and 1.2 Å grid resolution)
Contact:
Juan Fernandez-Recio (juanf AT bsc DOT es)
Daniel Jimenez-Gonzalez (djimenez AT ac DOT upc DOT edu)