Flexible framework of computing binding free energy using the energy representation theory of solution
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arXiv
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| Auteurs principaux: | Okita, Kazuya, Maruyama, Yusei, Kasahara, Kento, Matubayasi, Nobuyuki |
|---|---|
| Format: | Preprint |
| Publié: |
2024
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| Sujets: | |
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