ArticleSource code for biology and medicine2013
MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments.
Article in Source code for biology and medicine, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed, 26 citations in OpenAlex.
- Specificity of broad protein interaction surfaces for proteins with multiple binding partners.Biophysics and physicobiology · 2016Article
- Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures.BMC systems biology · 2015Article
- MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.Bioinformatics (Oxford, England) · 2014Article
- Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology.Molecular informatics · 2014Review
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProtein-protein interaction (PPI) plays a core role in cellular functions. Massively parallel supercomputing systems have been actively developed over the past few years, which enable large-scale biological problems to be solved, such as PPI network prediction based on tertiary structures.
resultsWe have developed a high throughput and ultra-fast PPI prediction system based on rigid docking, "MEGADOCK", by employing a hybrid parallelization (MPI/OpenMP) technique assuming usages on massively parallel supercomputing systems. MEGADOCK displays significantly faster processing speed in the rigid-body docking process that leads to full utilization of protein tertiary structural data for large-scale and network-level problems in systems biology. Moreover, the system was scalable as shown by measurements carried out on two supercomputing environments. We then conducted prediction of biological PPI networks using the post-docking analysis.
conclusionsWe present a new protein-protein docking engine aimed at exhaustive docking of mega-order numbers of protein pairs. The system was shown to be scalable by running on thousands of nodes. The software package is available at: http://www.bi.cs.titech.ac.jp/megadock/k/.
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Registered trials
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