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. 2010 Jul;38(Web Server issue):W445-9.
doi: 10.1093/nar/gkq311. Epub 2010 May 5.

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

Gary Macindoe  1 , Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W Ritchie
Affiliations

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

Gary Macindoe et al. Nucleic Acids Res. 2010 Jul.

Abstract

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 approximately 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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Figures

Figure 1.
Figure 1.
Screenshots of the two dataentry web pages of the HexServer interface. (A) Top: the first web page is used to specify the PDB files to be uploaded, and the type of docking calculation to be performed. (B) Bottom: the second web page may be used to define optional interface residues and angular search ranges to focus the search around a known or hypothesized interface. By convention, the larger of the two proteins is called the ‘receptor’ and the smaller is called the ‘ligand,’ although Hex treats the two proteins equally. All input parameters are explained in further detail in the online Help page, and some typical protein domains are available from the ‘Examples’ page.
Figure 2.
Figure 2.
A screenshot of a results page generated by HexServer.
See this image and copyright information in PMC

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