Letter to Editor: Accelerating atomistic refinement of NMR structures using Graphics Processing Unit
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we showed a dramatic acceleration of GBIS calculations by using GPU, which almost compensates the longer computational times required for GBIS. To the best of our knowledge, this is the first report of using GPU for refining the NMR structures. The 1500 ps calculation for 100 structures would be one of the longest atomistic refinements. This approach would permit a wider use of GBIS, even on moderately expensive hardware. GPU-accelerated GBIS could be particularly useful for biomolecules whose structures are difficult to determine by conventional NMR methods, such as membrane proteins and protein–protein complexes. It is difficult to obtain sufficient experimental restraints in the cases. The calculations with HN-HN restraints may approximate the situations. In this study, rSA was used for searching conformational space. One can combine sophisticated algorithm such as replica exchange17 with GPU instead. Our results will be a meaningful guideline in applying GPU-based acceleration into calculating NMR structure.
Abstract
we showed a dramatic acceleration of GBIS calculations by using GPU, which almost compensates the longer computational times required for GBIS. To the best of our knowledge, this is the first report of using GPU for refining the NMR structures. The 1500 ps calculation for 100 structures would be one of the longest atomistic refinements. This approach would permit a wider use of GBIS, even on moderately expensive hardware. GPU-accelerated GBIS could be particularly useful for biomolecules whose structures are difficult to determine by conventional NMR methods, such as membrane proteins and protein–protein complexes. It is difficult to obtain sufficient experimental restraints in the cases. The calculations with HN-HN restraints may approximate the situations. In this study, rSA was used for searching conformational space. One can combine sophisticated algorithm such as replica exchange17 with GPU instead. Our results will be a meaningful guideline in applying GPU-based acceleration into calculating NMR structure.
참고문헌 (21)
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