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

Autores
Jenik, Michael; Mocskos, Esteban; Roitberg, Adrián E.; Turjanski, Adrián G.
Año de publicación
2010
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
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
Materia
Ciencias Informáticas
GPU
Biología estructural
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/152731

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spelling Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)Jenik, MichaelMocskos, EstebanRoitberg, Adrián E.Turjanski, Adrián G.Ciencias InformáticasGPUBiología estructuralSolving 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 Operativa2010info:eu-repo/semantics/conferenceObjectinfo:eu-repo/semantics/publishedVersionObjeto de conferenciahttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdf3313-3324http://sedici.unlp.edu.ar/handle/10915/152731enginfo:eu-repo/semantics/altIdentifier/url/http://39jaiio.sadio.org.ar/sites/default/files/39jaiio-hpc-12.pdfinfo:eu-repo/semantics/altIdentifier/issn/1851-9326info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:39:27Zoai:sedici.unlp.edu.ar:10915/152731Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:39:27.261SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)
title Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)
spellingShingle Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)
Jenik, Michael
Ciencias Informáticas
GPU
Biología estructural
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)
dc.creator.none.fl_str_mv Jenik, Michael
Mocskos, Esteban
Roitberg, Adrián E.
Turjanski, Adrián G.
author Jenik, Michael
author_facet Jenik, Michael
Mocskos, Esteban
Roitberg, Adrián E.
Turjanski, Adrián G.
author_role author
author2 Mocskos, Esteban
Roitberg, Adrián E.
Turjanski, Adrián G.
author2_role author
author
author
dc.subject.none.fl_str_mv Ciencias Informáticas
GPU
Biología estructural
topic Ciencias Informáticas
GPU
Biología estructural
dc.description.none.fl_txt_mv 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
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.
publishDate 2010
dc.date.none.fl_str_mv 2010
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