title: Cell-Dock: high-performance protein-protein docking.
abstract: CONCLUSIONS
  The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized fast Fourier transform (FFT) approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200×, while achieving results of similar quality.
  
  
  METHODS
  The source code is released under GNU General Public License version 2 and can be downloaded from http://mmb.pcb.ub.es/~cpons/Cell-Dock.
  
  
  BACKGROUND
  djimenez@ac.upc.edu or juanf@bsc.es
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
authors: Carles
authors: C
authors: Pons
authors: Daniel
authors: D
authors: Jiménez-González
authors: Cecilia
authors: C
authors: González-Álvarez
authors: Harald
authors: H
authors: Servat
authors: Daniel
authors: D
authors: Cabrera-Benítez
authors: Xavier
authors: X
authors: Aguilar
authors: Juan
authors: J
authors: Fernández-Recio
mesh_terms: D000465:Algorithms; D005583:Fourier Analysis; D062105:Molecular Docking Simulation / Q000379:methods*; D046912:Multiprotein Complexes / Q000737:chemistry*; D012984:Software
chemical_list: D046912:Multiprotein Complexes