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GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphic processors

Xueming Li, Nikolaus Grigorieff, Yifan Cheng
he W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, United States
Journal of Structural Biology, Volume 172, Issue 3, December 2010, Pages 407-412 (15 June 2010)

@article{li2010gpu,

   title={GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphic processors},

   author={Li, X. and Grigorieff, N. and Cheng, Y.},

   journal={Journal of Structural Biology},

   issn={1047-8477},

   year={2010},

   publisher={Elsevier}

}

Among all the factors that determine the resolution of a 3D reconstruction by single particle electron cryo-microscopy (cryoEM), the number of particle images used in the dataset plays a major role. More images generally yield better resolution, assuming the imaged protein complex is conformationally and compositionally homogeneous. To facilitate processing of very large datasets, we modified the computer program, FREALIGN, to execute the computationally most intensive procedures on Graphics Processing Units (GPUs). Using the modified program, the execution speed increased between 10 and 240-fold depending on the task performed by FREALIGN. Here we report the steps necessary to parallelize critical FREALIGN subroutines and evaluate its performance on computers with multiple GPUs.
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