Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013)
巻, 号, ページ
pp. 883-889
出版年月
2013年9月22日
出版者
和文:
英文:
Association for Computing Machinery
会議名称
和文:
英文:
ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013), 2nd International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio2013)
Protein-protein docking is a method for predicting the protein complex structure from monomeric protein structures. Because protein structural information has been increased and the application field has been expanded to more difficult ones such as interactome prediction, a faster protein-protein docking method has been eagerly demanded. MEGADOCK is fast protein-protein docking software but more acceleration is demanded for an interactome prediction, which is composed of millions of protein pairs. In this paper, we developed an ultra-fast protein-protein docking software named MEGADOCK-GPU by using general purpose GPU computing techniques. We implemented a system that utilizes all CPU cores and GPUs in a computation node. As results, MEGADOCK-GPU on 12 CPU cores and 3 GPUs achieved a calculation speed that was 37.0 times faster than MEGADOCK on 1 CPU core. The novel docking software will facilitate the application of docking techniques to assist large-scale protein interaction network analyses. MEGADOCK-GPU is freely available at http://www.bi.cs.titech.ac.jp/megadock/gpu/.
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