3D-RISM-AI: A Machine Learning Approach to Predict Protein–Ligand Binding Affinity Using 3D-RISM von Osaki, Kazu, Ekimoto, Toru, Yamane, Tsutomu, Ikeguchi, Mitsunori

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Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble von Kidera, Akinori, Moritsugu, Kei, Ekimoto, Toru, Ikeguchi, Mitsunori

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Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV‑2 3CL Protease von Moritsugu, Kei, Ekimoto, Toru, Ikeguchi, Mitsunori, Kidera, Akinori

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Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates von Hikiri, Simon, Yoshidome, Takashi, Ikeguchi, Mitsunori

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Structure of SARS-CoV-2 membrane protein essential for virus assembly von Zhang, Zhikuan, Nomura, Norimichi, Muramoto, Yukiko, Ekimoto, Toru, Uemura, Tomoko, Liu, Kehong, Yui, Moeko, Kono, Nozomu, Aoki, Junken, Ikeguchi, Mitsunori, Noda, Takeshi, Iwata, So, Ohto, Umeharu, Shimizu, Toshiyuki

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Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations von Ekimoto, Toru, Kudo, Takafumi, Yamane, Tsutomu, Ikeguchi, Mitsunori

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A synthetic ion channel with anisotropic ligand response von Muraoka, Takahiro, Noguchi, Daiki, Kasai, Rinshi S., Sato, Kohei, Sasaki, Ryo, Tabata, Kazuhito V., Ekimoto, Toru, Ikeguchi, Mitsunori, Kamagata, Kiyoto, Hoshino, Norihisa, Noji, Hiroyuki, Akutagawa, Tomoyuki, Ichimura, Kazuaki, Kinbara, Kazushi

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Comprehensive 3D‐RISM analysis of the hydration of small molecule binding sites in ligand‐free protein structures von Yoshidome, Takashi, Ikeguchi, Mitsunori, Ohta, Masateru

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gr Predictor: A Deep Learning Model for Predicting the Hydration Structures around Proteins von Kawama, Kosuke, Fukushima, Yusaku, Ikeguchi, Mitsunori, Ohta, Masateru, Yoshidome, Takashi

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Effect of Water Molecules on the Activating S810L Mutation of the Mineralocorticoid Receptor von Takedomi, Kei, Ohta, Masateru, Ekimoto, Toru, Ikeguchi, Mitsunori

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TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction von Sakaniwa, Kentaro, Fujimura, Akiko, Shibata, Takuma, Shigematsu, Hideki, Ekimoto, Toru, Yamamoto, Masaki, Ikeguchi, Mitsunori, Miyake, Kensuke, Ohto, Umeharu, Shimizu, Toshiyuki

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Mechanism of the αβ Conformational Change in F1-ATPase after ATP Hydrolysis: Free-Energy Simulations von Ito, Yuko, Ikeguchi, Mitsunori

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Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane von Sato, Kohei, Sasaki, Ryo, Matsuda, Ryoto, Nakagawa, Mayuko, Ekimoto, Toru, Yamane, Tsutomu, Ikeguchi, Mitsunori, Tabata, Kazuhito V., Noji, Hiroyuki, Kinbara, Kazushi

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Hydration properties of a protein at low and high pressures: Physics of pressure denaturation von Inoue, Masao, Hayashi, Tomohiko, Hikiri, Simon, Ikeguchi, Mitsunori, Kinoshita, Masahiro

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Real-time tracking reveals catalytic roles for the two DNA binding sites of Rad51 von Ito, Kentaro, Murayama, Yasuto, Kurokawa, Yumiko, Kanamaru, Shuji, Kokabu, Yuichi, Maki, Takahisa, Mikawa, Tsutomu, Argunhan, Bilge, Tsubouchi, Hideo, Ikeguchi, Mitsunori, Takahashi, Masayuki, Iwasaki, Hiroshi

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Force‐field parametrization based on radial and energy distribution functions von Chiba, Shuntaro, Okuno, Yasushi, Honma, Teruki, Ikeguchi, Mitsunori

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Machine learning to estimate the local quality of protein crystal structures von Miyaguchi, Ikuko, Sato, Miwa, Kashima, Akiko, Nakagawa, Hiroyuki, Kokabu, Yuichi, Ma, Biao, Matsumoto, Shigeyuki, Tokuhisa, Atsushi, Ohta, Masateru, Ikeguchi, Mitsunori

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Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method von Ekimoto, Toru, Yamane, Tsutomu, Ikeguchi, Mitsunori

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Structural analysis reveals TLR7 dynamics underlying antagonism von Tojo, Shingo, Zhang, Zhikuan, Matsui, Hiroyuki, Tahara, Masahiro, Ikeguchi, Mitsunori, Kochi, Mami, Kamada, Mami, Shigematsu, Hideki, Tsutsumi, Akihisa, Adachi, Naruhiko, Shibata, Takuma, Yamamoto, Masaki, Kikkawa, Masahide, Senda, Toshiya, Isobe, Yoshiaki, Ohto, Umeharu, Shimizu, Toshiyuki

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Development of the force field for cyclosporine A von Yamane, Tsutomu, Ekimoto, Toru, Ikeguchi, Mitsunori

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