title: Using graphics processors to accelerate protein docking calculations.
abstract: Protein docking is the computationally intensive task of calculating the three-dimensional structure of a protein complex starting from the individual structures of the constituent proteins. In order to make the calculation tractable, most docking algorithms begin by assuming that the structures to be docked are rigid. This article describes some recent developments we have made to adapt our FFT-based "Hex" rigid-body docking algorithm to exploit the computational power of modern graphics processors (GPUs). The Hex algorithm is very efficient on conventional central processor units (CPUs), yet significant further speed-ups have been obtained by using GPUs. Thus, FFT-based docking calculations which formerly took many hours to complete using CPUs may now be carried out in a matter of seconds using GPUs. The Hex docking program and access to a server version of Hex on a GPU-based compute cluster are both available for public use.
authors.affiliation: Orpailleur Team, INRIA Nancy - Grand Est, LORIA, 615 Rue du Jardin Botanique, 54506 Vandoeuvre-lès-Nancy, France.
authors.forename: David W
authors.initials: DW
authors.lastname: Ritchie
authors.forename: Vishwesh
authors.initials: V
authors.lastname: Venkatraman
authors.forename: Lazaros
authors.initials: L
authors.lastname: Mavridis
mesh_terms: D003626:Data Display; D008491:Medical Informatics Applications; D011485:Protein Binding; D025941:Protein Interaction Mapping; D011506:Proteins / Q000378:metabolism; D012985:Software Design
chemical_list: D011506:Proteins