A 281 Tflops calculation for X-ray protein structure analysis with special-purpose computers MDGRAPE-3

Yousuke Ohno, Eiji Nishibori, Tetsu Narumi, Takahiro Koishi, Tahir H. Tahirov, Hideo Ago, Masashi Miyano, Ryutaro Himeno, Toshikazu Ebisuzaki, Makoto Sakata, Makoto Taiji

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Citations (Scopus)

Abstract

We have achieved a sustained calculation speed of 281 Tflops for the optimization of the 3-D structures of proteins from the X-ray experimental data by the Genetic Algorithm - Direct Space (GA-DS) method. In this calculation we used MDGRAPE-3, special-purpose computer for molecular simulations, with the peak performance of 752 Tflops. In the GA-DS method, a set of selected parameters which define the crystal structures of proteins is optimized by the Genetic Algorithm. As a criterion to estimate the model parameters, we used the reliability factor R1 which indicates the statistical difference between the calculated and the measured diffraction data. To evaluate this factor it is necessary to reconstruct the diffraction patterns of the model structures every time the model is updated. Therefore, in this method the nonequispaced Discrete Fourier Transformation (DFT) used to calculate the diffraction patterns dominates most of the computation time. To accelerate DFT calculations, we used the special-purpose computer, MDGRAPE-3. A molecule, Carbamoyl-Phosphate Synthetase was investigated. The final reliability factors were much smaller than the typical values obtained in other methods such as the Molecular Replacement (MR) method. Our results successfully demonstrate that high-performance computing with GA-DS method on special-purpose computers is effective for the structure determination of biological molecules and the method has a potential to be widely used in near future. (c) 2007 ACM.

Original languageEnglish (US)
Title of host publicationProceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07
DOIs
StatePublished - Dec 1 2007
Event2007 ACM/IEEE Conference on Supercomputing, SC'07 - Reno, NV, United States
Duration: Nov 10 2007Nov 16 2007

Publication series

NameProceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07

Conference

Conference2007 ACM/IEEE Conference on Supercomputing, SC'07
CountryUnited States
CityReno, NV
Period11/10/0711/16/07

Fingerprint

Genetic algorithms
Proteins
X rays
Diffraction patterns
Molecules
Model structures
Phosphates
Diffraction
Crystal structure

Keywords

  • Genetic algorithm
  • Special-purpose computer
  • X-ray structure determination

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Software
  • Electrical and Electronic Engineering

Cite this

Ohno, Y., Nishibori, E., Narumi, T., Koishi, T., Tahirov, T. H., Ago, H., ... Taiji, M. (2007). A 281 Tflops calculation for X-ray protein structure analysis with special-purpose computers MDGRAPE-3. In Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07 [56] (Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07). https://doi.org/10.1145/1362622.1362698

A 281 Tflops calculation for X-ray protein structure analysis with special-purpose computers MDGRAPE-3. / Ohno, Yousuke; Nishibori, Eiji; Narumi, Tetsu; Koishi, Takahiro; Tahirov, Tahir H.; Ago, Hideo; Miyano, Masashi; Himeno, Ryutaro; Ebisuzaki, Toshikazu; Sakata, Makoto; Taiji, Makoto.

Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07. 2007. 56 (Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Ohno, Y, Nishibori, E, Narumi, T, Koishi, T, Tahirov, TH, Ago, H, Miyano, M, Himeno, R, Ebisuzaki, T, Sakata, M & Taiji, M 2007, A 281 Tflops calculation for X-ray protein structure analysis with special-purpose computers MDGRAPE-3. in Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07., 56, Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07, 2007 ACM/IEEE Conference on Supercomputing, SC'07, Reno, NV, United States, 11/10/07. https://doi.org/10.1145/1362622.1362698
Ohno Y, Nishibori E, Narumi T, Koishi T, Tahirov TH, Ago H et al. A 281 Tflops calculation for X-ray protein structure analysis with special-purpose computers MDGRAPE-3. In Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07. 2007. 56. (Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07). https://doi.org/10.1145/1362622.1362698
Ohno, Yousuke ; Nishibori, Eiji ; Narumi, Tetsu ; Koishi, Takahiro ; Tahirov, Tahir H. ; Ago, Hideo ; Miyano, Masashi ; Himeno, Ryutaro ; Ebisuzaki, Toshikazu ; Sakata, Makoto ; Taiji, Makoto. / A 281 Tflops calculation for X-ray protein structure analysis with special-purpose computers MDGRAPE-3. Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07. 2007. (Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07).
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