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In this calculation we used MDGRAPE-3, special-purpose computer for molecular simulations, with the peak performance of 752 Tflops. ... 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 ... Acknowledgement We thank A. Suenaga, N. Okimoto and N. Futatsugi for the development of MDGRAPE-3. E. N. M. S. thanks S. Natsume for the help in development of GA -DS system. E. N. and M. S. thank M. ...doi:10.1145/1362622.1362698 dblp:conf/sc/OhnoNNKTAMHEST07 fatcat:nuxu7fvdbjhzfou7btd4dfkiee