MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers

Summary: The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous super...

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Autores principales: Ohue, Masahito, Shimoda, Takehiro, Suzuki, Shuji, Matsuzaki, Yuri, Ishida, Takashi, Akiyama, Yutaka
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221127/
https://www.ncbi.nlm.nih.gov/pubmed/25100686
http://dx.doi.org/10.1093/bioinformatics/btu532
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author Ohue, Masahito
Shimoda, Takehiro
Suzuki, Shuji
Matsuzaki, Yuri
Ishida, Takashi
Akiyama, Yutaka
author_facet Ohue, Masahito
Shimoda, Takehiro
Suzuki, Shuji
Matsuzaki, Yuri
Ishida, Takashi
Akiyama, Yutaka
author_sort Ohue, Masahito
collection PubMed
description Summary: The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of >97% strong scaling. Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock. Contact: akiyama@cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online
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spelling pubmed-42211272014-11-10 MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers Ohue, Masahito Shimoda, Takehiro Suzuki, Shuji Matsuzaki, Yuri Ishida, Takashi Akiyama, Yutaka Bioinformatics Applications Notes Summary: The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of >97% strong scaling. Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock. Contact: akiyama@cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online Oxford University Press 2014-11-15 2014-08-06 /pmc/articles/PMC4221127/ /pubmed/25100686 http://dx.doi.org/10.1093/bioinformatics/btu532 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Ohue, Masahito
Shimoda, Takehiro
Suzuki, Shuji
Matsuzaki, Yuri
Ishida, Takashi
Akiyama, Yutaka
MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers
title MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers
title_full MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers
title_fullStr MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers
title_full_unstemmed MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers
title_short MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers
title_sort megadock 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221127/
https://www.ncbi.nlm.nih.gov/pubmed/25100686
http://dx.doi.org/10.1093/bioinformatics/btu532
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