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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Detalles Bibliográficos
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
Descripción
Sumario: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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