Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)

Solving the structure of protein-protein complexes is one of the most important tasks in structural biology. Even though there has been great progress in recent years there still a small number of protein complexes structures deposited in the Protein Data Bank in comparison to isolated partners. In...

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Detalles Bibliográficos
Autores principales: Jenik, Michael, Mocskos, Esteban, Roitberg, Adrián E., Turjanski, Adrián G.
Formato: Objeto de conferencia
Lenguaje:Inglés
Publicado: 2010
Materias:
Ciencias Informáticas
GPU
Biología estructural
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/152731
http://39jaiio.sadio.org.ar/sites/default/files/39jaiio-hpc-12.pdf
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-152731
record_format dspace
spelling I19-R120-10915-1527312023-05-10T20:02:56Z http://sedici.unlp.edu.ar/handle/10915/152731 http://39jaiio.sadio.org.ar/sites/default/files/39jaiio-hpc-12.pdf issn:1851-9326 Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU) Jenik, Michael Mocskos, Esteban Roitberg, Adrián E. Turjanski, Adrián G. 2010 2010 2023-05-10T16:53:35Z en Ciencias Informáticas GPU Biología estructural Solving the structure of protein-protein complexes is one of the most important tasks in structural biology. Even though there has been great progress in recent years there still a small number of protein complexes structures deposited in the Protein Data Bank in comparison to isolated partners. In this sense, the computational prediction of protein complexes starting from the unbound structures, protein-protein Docking algorithms, has emerged as a reasonable alternative. Many docking programs employ Fast Fourier Transform (FFT) correlations as an efficient search strategy. We describe an implementation of a protein-protein docking program based on FFT surface complementarity that runs entirely on a Graphics Processing Unit (GPU), including grid generation, rotation and scoring. We evaluate its performance, and show that it can be up to 13 times faster than conventional CPU based implementations. Sociedad Argentina de Informática e Investigación Operativa Objeto de conferencia Objeto de conferencia http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf 3313-3324
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Ciencias Informáticas
GPU
Biología estructural
spellingShingle Ciencias Informáticas
GPU
Biología estructural
Jenik, Michael
Mocskos, Esteban
Roitberg, Adrián E.
Turjanski, Adrián G.
Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)
topic_facet Ciencias Informáticas
GPU
Biología estructural
description Solving the structure of protein-protein complexes is one of the most important tasks in structural biology. Even though there has been great progress in recent years there still a small number of protein complexes structures deposited in the Protein Data Bank in comparison to isolated partners. In this sense, the computational prediction of protein complexes starting from the unbound structures, protein-protein Docking algorithms, has emerged as a reasonable alternative. Many docking programs employ Fast Fourier Transform (FFT) correlations as an efficient search strategy. We describe an implementation of a protein-protein docking program based on FFT surface complementarity that runs entirely on a Graphics Processing Unit (GPU), including grid generation, rotation and scoring. We evaluate its performance, and show that it can be up to 13 times faster than conventional CPU based implementations.
format Objeto de conferencia
Objeto de conferencia
author Jenik, Michael
Mocskos, Esteban
Roitberg, Adrián E.
Turjanski, Adrián G.
author_facet Jenik, Michael
Mocskos, Esteban
Roitberg, Adrián E.
Turjanski, Adrián G.
author_sort Jenik, Michael
title Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)
title_short Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)
title_full Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)
title_fullStr Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)
title_full_unstemmed Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)
title_sort accelerating protein-protein docking using a graphics processing unit (gpu)
publishDate 2010
url http://sedici.unlp.edu.ar/handle/10915/152731
http://39jaiio.sadio.org.ar/sites/default/files/39jaiio-hpc-12.pdf
work_keys_str_mv AT jenikmichael acceleratingproteinproteindockingusingagraphicsprocessingunitgpu
AT mocskosesteban acceleratingproteinproteindockingusingagraphicsprocessingunitgpu
AT roitbergadriane acceleratingproteinproteindockingusingagraphicsprocessingunitgpu
AT turjanskiadriang acceleratingproteinproteindockingusingagraphicsprocessingunitgpu
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