タンパク質立体構造モデリングプログラム実行速度の高速化

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  • Speedup of the protein tertiary structure modeling program execution speed

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Three speedup actions had performed in homology modeling method, FAMS. One of them is multi-thread to have functioned. The relationship between the degree of speedup and the number of the threads is non-liner. The reason of the non-linearity is regarded as having adopted fork function. The structure body array for many amino acid residues included in the protein was declared in the original version of FAMS software, and it requires considerable memory. Additionally, fork function makes full memory duplicate to all co-processes. The duplication affects the total spending time in multi-threading steps. Therefore, array size reduction or appropriate selection of variables is required.

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