Computational Exploration of Minimum Energy Reaction Pathway of N2O Formation from Intermediate I of P450nor Using an Active Center Model von Kanematsu, Yusuke, Kondo, Hiroko X., Takano, Yu

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Depolarizing Effects in Hydrogen Bond Energy in 310-Helices Revealed by Quantum Chemical Analysis von Kondo, Hiroko X., Nakamura, Haruki, Takano, Yu

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Random Forest Classifier of Heme Proteins Using Porphyrin Distortions and Axial Ligands of Heme von Fujikawa, Hinako, Kondo, Hiroko X., Kanematsu, Yusuke, Takano, Yu

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Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket von Kondo, Hiroko X, Fujii, Masanori, Tanioka, Takuma, Kanematsu, Yusuke, Yoshida, Takashi, Takano, Yu

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PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins von Kondo, Hiroko X, Kanematsu, Yusuke, Masumoto, Gen, Takano, Yu

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Quantum chemical studies on hydrogen bonds in helical secondary structures von Takano, Yu, Kondo, Hiroko X., Nakamura, Haruki

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Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin von Kondo, Hiroko X, Takano, Yu

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Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations von Nakayoshi, Tomoki, Ohnishi, Yusuke, Tanaka, Hideaki, Kurisu, Genji, Kondo, Hiroko X, Takano, Yu

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Zn2+-Binding to the Voltage-Gated Proton Channel Hv1/VSOP von Iwaki, Masayo, Takeshita, Kohei, Kondo, Hiroko X, Kinoshita, Kengo, Okamura, Yasushi, Takano, Yu, Nakagawa, Atsushi, Kandori, Hideki

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Conformational Preference of Flavonols and Its Effect on the Chemical Properties Involved in Radical Scavenging Activity von Kondo, Hiroko X., Takano, Yu

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The evolutionary process of mammalian sex determination genes focusing on marsupial SRYs von Katsura, Yukako, Kondo, Hiroko X, Ryan, Janelle, Harley, Vincent, Satta, Yoko

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Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG16 von Kondo, Hiroko X., Kiribayashi, Ryo, Kuroda, Daisuke, Kohda, Jiro, Kugimiya, Akimitsu, Nakano, Yasuhisa, Tsumoto, Kouhei, Takano, Yu

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Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network von Kondo, Hiroko X, Iizuka, Hiroyuki, Masumoto, Gen, Kabaya, Yuichi, Kanematsu, Yusuke, Takano, Yu

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Enhanced exchange algorithm without detailed balance condition for replica exchange method von Kondo, Hiroko X, Taiji, Makoto

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Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network von Kondo, Hiroko X, Iizuka, Hiroyuki, Masumoto, Gen, Kabaya, Yuichi, Kanematsu, Yusuke, Takano, Yu

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Structure comparison of heme-binding sites in heme protein predicted by AlphaFold3 and AlphaFold2 von Kondo, Hiroko X, Takano, Yu

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Quantitative evaluation of noncovalent interactions with negative fragmentation approach including basis set superposition error correction von Takano, Yu, Kondo, Hiroko X, Nakamura, Haruki

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Structure of Heme-binding Pocket in Heme Protein is Generally Rigid and can be Predicted by AlphaFold2 von Kondo, Hiroko X, Kanematsu, Yusuke, Takano, Yu

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Free-Energy Landscapes of Protein Domain Movements upon Ligand Binding von Kondo, Hiroko X, Okimoto, Noriaki, Morimoto, Gentaro, Taiji, Makoto

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Statistical and quantum-chemical analysis of the effect of heme porphyrin distortion in heme proteins: Differences between oxidoreductases and oxygen carrier proteins von Kanematsu, Yusuke, Kondo, Hiroko X., Imada, Yasuhiro, Takano, Yu

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