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Usage Examples

Target Reward Config Additional requirement Ref.
LogP logP_reward.py setting.yaml - -
Jscore Jscore_reward.py setting_jscore.yaml - 1
Absorption wavelength chro_reward.py setting_chro.yaml Gaussian 162
via QCforever9		 3
Absorption wavelength chro_gamess_reward.py setting_chro_gamess.yaml GAMESS 2022.211 via QCforever9
Upper-absorption & fluorescence
wavelength		 fluor_reward.py setting_fluor.yaml Gaussian 162
via QCforever9		 4
Kinase inhibitory activities dscore_reward.py setting_dscore.yaml LightGBM5 6
Docking score Vina_binary_reward.py setting_vina_binary.yaml AutoDock Vina7 8
Pharmacophore pharmacophore_reward.py setting_pharmacophore.yaml - 10
gnina docking gnina_singularity_reward.py setting_gnina_singularity.yaml - -
Linker generation Linker_logP_reward.py setting_linker.yaml - -

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  6. Yoshizawa, T., Ishida, S., Sato, T., Ohta, M., Honma, T., & Terayama, K. (2022). Selective Inhibitor Design for Kinase Homologs Using Multiobjective Monte Carlo Tree Search. Journal of Chemical Information and Modeling, 62(22), 5351–5360. https://doi.org/10.1021/acs.jcim.2c00787 ↩

  7. Eberhardt, J., Santos-Martins, D., Tillack, A. F., & Forli, S. (2021). AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. Journal of Chemical Information and Modeling, 61(8), 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203 ↩

  8. Ma, B., Terayama, K., Matsumoto, S., Isaka, Y., Sasakura, Y., Iwata, H., Araki, M., & Okuno, Y. (2021). Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations. Journal of Chemical Information and Modeling, 61(7), 3304–3313. https://doi.org/10.1021/acs.jcim.1c00679 ↩

  9. Sumita, M., Terayama, K., Tamura, R., & Tsuda, K. (2022). QCforever: A Quantum Chemistry Wrapper for Everyone to Use in Black-Box Optimization. Journal of Chemical Information and Modeling, 62(18), 4427–4434. https://doi.org/10.1021/acs.jcim.2c00812 ↩↩↩

  10. 石田祥一, 吉澤竜哉, 寺山慧 (2023). 深層学習と木探索に基づくde novo分子設計, SAR News, 44. ↩

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