HexServer: an FFT-based protein docking server powered by graphics processors

Gary Macindoe (1) , Lazaros Mavridis (2) , Vishwesh Venkatraman (2) , Marie-Dominique Devignes (2) , David Ritchie (2)

1 School of Computing Science [Glasgow]
2 ORPAILLEUR - Knowledge representation, reasonning

HexServer (http://hexserver.loria.fr/) is the first FFT-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical six-dimensional docking run takes around 15 seconds, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions. The server requires two protein structures in PDB format to be uploaded, and it produces a ranked list of up to 1000 docking predictions. Knowledge of one or both protein binding sites may be used to focus and shorten the calculation when such information is available. The first 20 predictions may be accessed individually, and a single file of all predicted orientations may be down-loaded as a compressed multi-model PDB file. The server is publicly available and does not require any registration or identification by the user.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David Ritchie. HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Research, 2010, 38, pp.W445-W449. ⟨10.1093/nar/gkq311⟩. ⟨inria-00522712⟩