ArticleBMC systems biology2015
Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures.
Article in BMC systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- In Silico Structural Modeling and Analysis of Elongation Factor-1 Alpha and Elongation Factor-like Protein.ACS omega · 2019Article
- Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking.Journal of computational chemistry · 2018Article
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Authors and funding
5 authors.
Funding
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Abstract
backgroundThe hardware accelerators will provide solutions to computationally complex problems in bioinformatics fields. However, the effect of acceleration depends on the nature of the application, thus selection of an appropriate accelerator requires some consideration.
resultsIn the present study, we compared the effects of acceleration using graphics processing unit (GPU) and many integrated core (MIC) on the speed of fast Fourier transform (FFT)-based protein-protein docking calculation. The GPU implementation performed the protein-protein docking calculations approximately five times faster than the MIC offload mode implementation. The MIC native mode implementation has the advantage in the implementation costs. However, the performance was worse with larger protein pairs because of memory limitations.
conclusionThe results suggest that GPU is more suitable than MIC for accelerating FFT-based protein-protein docking applications.
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