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Low cost, high performance GPU computing solution for atomic resolution cryoEM single-particle reconstruction

Xiaokang Zhang, Xing Zhang, Z. Hong Zhou
Hefei National Laboratory for Physical Sciences at Nanoscale, University of Science and Technology of China, Hefei 230027, China
Journal of Structural Biology, Volume 172, Issue 3, December 2010, Pages 400-406 (21 May 2010)

@article{zhang2010low,

   title={Low Cost, High Performance GPU Computing Solution for Atomic Resolution CryoEM Single-Particle Reconstruction},

   author={Zhang, X. and Zhang, X. and Zhou, Z.H.},

   journal={Journal of Structural Biology},

   issn={1047-8477},

   year={2010},

   publisher={Elsevier}

}

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Recent advancements in cryo-electron microscopy (cryoEM) have made it technically possible to determine the three-dimensional (3D) structures of macromolecular complexes at atomic resolution. However, processing the large amount of data needed for atomic resolution reconstructions requires either accessing to very expensive computer clusters or waiting for weeks of continuous computation in a personal computer (PC). In this paper, we present a practical computational solution to this 3D reconstruction problem through the optimal utilization of the processing capabilities of both commodity graphics hardware (i.e., general purpose graphics processing unit (GPGPU)). Our solution, which is implemented in a new program, called eLite3D , has a number of advanced features of general interests. We construct interleaved schemes to prevent the data race condition intrinsic in merging of 2D data into a 3D volume. The speedup of eLite3D is up to 100 times over other commonly used 3D reconstruction programs with the same accuracy, thus allowing completion of atomic resolution 3D reconstructions of large complexes in a PC in 1-2
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