MEGADOCK 4.0：一款用于异构超级计算机的超高性能蛋白质-蛋白质对接软件。
MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.
机构信息
Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
出版信息
Bioinformatics. 2014 Nov 15;30(22):3281-3. doi: 10.1093/bioinformatics/btu532. Epub 2014 Aug 6.
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
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
蛋白质-蛋白质对接在大规模互作组分析中的应用是结构生物信息学的一个主要挑战，需要大量的计算资源。在这项工作中，我们提出了基于 FFT 的对接软件 MEGADOCK 4.0，它广泛利用了最新的异构超级计算机，并表现出强大的、可扩展的性能，>97%的强扩展性。
可用性和实现
MEGADOCK 4.0 是用 C++编写的，使用 OpenMPI 和 NVIDIA CUDA 5.0（或更高版本），并可在以下网址免费提供给所有学术和非营利用户：http://www.bi.cs.titech.ac.jp/megadock。
联系方式
补充信息
补充数据可在 Bioinformatics 在线获得。
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