InforLorV4, PascalFrancis, Corpus, bibRecord, 000201

Ultra-fast FFT protein docking on graphics processors

Identifieur interne : 000201 ( PascalFrancis/Corpus ); précédent : 000200; suivant : 000202

Ultra-fast FFT protein docking on graphics processors

Auteurs : David W. Ritchie ; Vishwesh Venkatraman

Source :

Bioinformatics : (Oxford. Print) [ 1367-4803 ] ; 2010.

RBID : Pascal:10-0462559

Descripteurs français

Pascal (Inist)
- Protéine, Arrimage, Représentation graphique.

English descriptors

KwdEn :
- Docking, Graphics, Protein.

Abstract

Motivation: Modelling protein-protein interactions (PPIs) is an increasingly important aspect of structural bioinformatics. However, predicting PPIs using in silico docking techniques is computationally very expensive. Developing very fast protein docking tools will be useful for studying large-scale PPI networks, and could contribute to the rational design of new drugs. Results: The Hex spherical polar Fourier protein docking algorithm has been implemented on Nvidia graphics processor units (GPUs). On a GTX 285 GPU, an exhaustive and densely sampled 6D docking search can be calculated in just 15 s using multiple 1D fast Fourier transforms (FFTs). This represents a 45-fold speed-up over the corresponding calculation on a single CPU, being at least two orders of magnitude times faster than a similar CPU calculation using ZDOCK 3.0.1, and estimated to be at least three orders of magnitude faster than the GPU-accelerated version of PIPER on comparable hardware. Hence, for the first time, exhaustive FFT-based protein docking calculations may now be performed in a matter of seconds on a contemporary GPU. Three-dimensional Hex FFT correlations are also accelerated by the GPU, but the speed-up factor of only 2.5 is much less than that obtained with 1 D FFTs. Thus, the Hex algorithm appears to be especially well suited to exploit GPUs compared to conventional 3D FFT docking approaches. Availability: http://hex.loria.fr/ and http://hexserver.loria.fr/ Contact: dave.ritchie@loria.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Notice en format standard (ISO 2709)

Pour connaître la documentation sur le format Inist Standard.

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C01	`01`		`ENG`	@0 Motivation: Modelling protein-protein interactions (PPIs) is an increasingly important aspect of structural bioinformatics. However, predicting PPIs using in silico docking techniques is computationally very expensive. Developing very fast protein docking tools will be useful for studying large-scale PPI networks, and could contribute to the rational design of new drugs. Results: The Hex spherical polar Fourier protein docking algorithm has been implemented on Nvidia graphics processor units (GPUs). On a GTX 285 GPU, an exhaustive and densely sampled 6D docking search can be calculated in just 15 s using multiple 1D fast Fourier transforms (FFTs). This represents a 45-fold speed-up over the corresponding calculation on a single CPU, being at least two orders of magnitude times faster than a similar CPU calculation using ZDOCK 3.0.1, and estimated to be at least three orders of magnitude faster than the GPU-accelerated version of PIPER on comparable hardware. Hence, for the first time, exhaustive FFT-based protein docking calculations may now be performed in a matter of seconds on a contemporary GPU. Three-dimensional Hex FFT correlations are also accelerated by the GPU, but the speed-up factor of only 2.5 is much less than that obtained with 1 D FFTs. Thus, the Hex algorithm appears to be especially well suited to exploit GPUs compared to conventional 3D FFT docking approaches. Availability: http://hex.loria.fr/ and http://hexserver.loria.fr/ Contact: dave.ritchie@loria.fr Supplementary information: Supplementary data are available at Bioinformatics online.
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Format Inist (serveur)

NO :	PASCAL 10-0462559 INIST
ET :	Ultra-fast FFT protein docking on graphics processors
AU :	RITCHIE (David W.); VENKATRAMAN (Vishwesh)
AF :	INRIA Nancy-Grand Est, LORIA, 615 Rue du Jardin Botanique/54506 Vandoeuvre-lès-Nancy/France (1 aut., 2 aut.)
DT :	Publication en série; Niveau analytique
SO :	Bioinformatics : (Oxford. Print); ISSN 1367-4803; Royaume-Uni; Da. 2010; Vol. 26; No. 19; Pp. 2398-2405; Bibl. 3/4 p.
LA :	Anglais
EA :	Motivation: Modelling protein-protein interactions (PPIs) is an increasingly important aspect of structural bioinformatics. However, predicting PPIs using in silico docking techniques is computationally very expensive. Developing very fast protein docking tools will be useful for studying large-scale PPI networks, and could contribute to the rational design of new drugs. Results: The Hex spherical polar Fourier protein docking algorithm has been implemented on Nvidia graphics processor units (GPUs). On a GTX 285 GPU, an exhaustive and densely sampled 6D docking search can be calculated in just 15 s using multiple 1D fast Fourier transforms (FFTs). This represents a 45-fold speed-up over the corresponding calculation on a single CPU, being at least two orders of magnitude times faster than a similar CPU calculation using ZDOCK 3.0.1, and estimated to be at least three orders of magnitude faster than the GPU-accelerated version of PIPER on comparable hardware. Hence, for the first time, exhaustive FFT-based protein docking calculations may now be performed in a matter of seconds on a contemporary GPU. Three-dimensional Hex FFT correlations are also accelerated by the GPU, but the speed-up factor of only 2.5 is much less than that obtained with 1 D FFTs. Thus, the Hex algorithm appears to be especially well suited to exploit GPUs compared to conventional 3D FFT docking approaches. Availability: http://hex.loria.fr/ and http://hexserver.loria.fr/ Contact: dave.ritchie@loria.fr Supplementary information: Supplementary data are available at Bioinformatics online.
CC :	002A01B
FD :	Protéine; Arrimage; Représentation graphique
ED :	Protein; Docking; Graphics
SD :	Proteína; Estiba; Grafo (curva)
LO :	INIST-21331.354000191303510060
ID :	10-0462559

Links to Exploration step

Pascal:10-0462559

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Ultra-fast FFT protein docking on graphics processors

Ultra-fast FFT protein docking on graphics processors

Source :

Descripteurs français

English descriptors

Abstract

Notice en format standard (ISO 2709)

Format Inist (serveur)

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri