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

Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie
Department of Computing Science, Lillybank Gardens, University of Glasgow, G12 8QQ Scotland, UK
Nucleic Acids Research, Volume 38, Issue suppl 2, p.W445-W449, 2010


   title={HexServer: an FFT-based protein docking server powered by graphics processors},

   author={Macindoe, G. and Mavridis, L. and Venkatraman, V. and Devignes, M.D. and Ritchie, D.W.},

   journal={Nucleic Acids Research},


   number={Web Server issue},




   publisher={Oxford Univ Press}


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HexServer (http://hexserver.loria.fr/) is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical 6D docking run takes ~15 s, 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 downloaded as a compressed multi-model PDB file. The server is publicly available and does not require any registration or identification by the user.
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