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

Gary Macindoe; Lazaros Mavridis; Vishwesh Venkatraman; Marie-Dominique Devignes; David W. Ritchie

doi:10.1093/nar/gkq311

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

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

School of Chemistry

Research output: Contribution to journal › Article › peer-review

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 similar to 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.

Original language	English
Pages (from-to)	W445-W449
Number of pages	5
Journal	Nucleic Acids Research
Volume	38
Issue number	Suppl 2
Early online date	5 May 2010
DOIs	https://doi.org/10.1093/nar/gkq311
Publication status	Published - Jul 2010

Keywords

HexServer
Fourier transform (FFT)-based protein docking server
Graphics processors

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10.1093/nar/gkq311

W445.full
© The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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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 similar to 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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HexServer: an FFT-based protein docking server powered by graphics processors

Abstract

Keywords

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