### 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 R_{1} 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 language | English (US) |
---|---|

Title of host publication | Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07 |

DOIs | |

State | Published - Dec 1 2007 |

Event | 2007 ACM/IEEE Conference on Supercomputing, SC'07 - Reno, NV, United States Duration: Nov 10 2007 → Nov 16 2007 |

### Publication series

Name | Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07 |
---|

### Conference

Conference | 2007 ACM/IEEE Conference on Supercomputing, SC'07 |
---|---|

Country | United States |

City | Reno, NV |

Period | 11/10/07 → 11/16/07 |

### Fingerprint

### 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

*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.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

*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

}

TY - GEN

T1 - A 281 Tflops calculation for X-ray protein structure analysis with special-purpose computers MDGRAPE-3

AU - Ohno, Yousuke

AU - Nishibori, Eiji

AU - Narumi, Tetsu

AU - Koishi, Takahiro

AU - Tahirov, Tahir H.

AU - Ago, Hideo

AU - Miyano, Masashi

AU - Himeno, Ryutaro

AU - Ebisuzaki, Toshikazu

AU - Sakata, Makoto

AU - Taiji, Makoto

PY - 2007/12/1

Y1 - 2007/12/1

N2 - 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.

AB - 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.

KW - Genetic algorithm

KW - Special-purpose computer

KW - X-ray structure determination

UR - http://www.scopus.com/inward/record.url?scp=56749182366&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=56749182366&partnerID=8YFLogxK

U2 - 10.1145/1362622.1362698

DO - 10.1145/1362622.1362698

M3 - Conference contribution

AN - SCOPUS:56749182366

SN - 9781595937643

T3 - Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07

BT - Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07

ER -