Publications by authors named "Yu Takano"

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Reduction-Induced Structural and Motional Changes of Plant-Type Ferredoxin Using Molecular Dynamics and Umbrella Sampling Simulations.
Tomoki Nakayoshi, Yusuke Ohnishi, Hideaki Tanaka, Genji Kurisu, Yu Takano

J Comput Chem· August 2025

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Image Findings of Breast Cancer-Related Elastosis: A Case Report.
Yu Takano, Shoji Oura, Mariko Honda

Case Rep Oncol· February 2025

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Computational Exploration of Minimum Energy Reaction Pathway of NO Formation from Intermediate of P450nor Using an Active Center Model.
Yusuke Kanematsu, Hiroko X Kondo, Yu Takano

Int J Mol Sci· December 2023

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Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals.
Artoni Kevin R Ang, Yasufumi Umena, Ayana Sato-Tomita, Naoya Shibayama, Naohisa Happo, Yu Takano

J Synchrotron Radiat· March 2023

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Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study.
Shunya Suenaga, Yu Takano, Toru Saito

Molecules· March 2023

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

Biomolecules· January 2023

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

Int J Mol Sci· December 2022

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

Biophys Rev· December 2022

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Structures and mechanisms of actin ATP hydrolysis.
Yusuke Kanematsu, Akihiro Narita, Toshiro Oda, Ryotaro Koike, Motonori Ota, Yu Takano

Proc Natl Acad Sci U S A· October 2022

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Depolarizing Effects in Hydrogen Bond Energy in 3-Helices Revealed by Quantum Chemical Analysis.
Hiroko X Kondo, Haruki Nakamura, Yu Takano

Int J Mol Sci· August 2022

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

Biomolecules· August 2022

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Predicting Reaction Mechanisms for the Threonine-Residue Stereoinversion Catalyzed by a Dihydrogen Phosphate Ion.
Tomoki Nakayoshi, Koichi Kato, Eiji Kurimoto, Yu Takano, Akifumi Oda

ACS Omega· June 2022

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Development of a one-step analysis method for several amino acids using a microfluidic paper-based analytical device.
Akimitsu Kugimiya, Sho Wakimoto, Jiro Kohda, Yasuhisa Nakano, Yu Takano

Sci Rep· March 2022

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QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease.
Toru Saito, Yu Takano

J Phys Chem B· March 2022

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

J Chem Inf Model· February 2022

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

Life (Basel)· January 2022

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Short-lived intermediate in NO generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography.
Takashi Nomura, Tetsunari Kimura, Yusuke Kanematsu, Daichi Yamada, Keitaro Yamashita, Yu Takano

Proc Natl Acad Sci U S A· May 2021

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Spin-projected QM/MM Free Energy Simulations for Oxidation Reaction of Guanine in B-DNA by Singlet Oxygen.
Toru Saito, Yu Takano

Chemphyschem· March 2021

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Microfluidic Paper-Based Analytical Device for Histidine Determination.
Akimitsu Kugimiya, Akane Fujikawa, Xiao Jiang, Z Hugh Fan, Toshikazu Nishida, Yu Takano

Appl Biochem Biotechnol· November 2020

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

Database (Oxford)· October 2020

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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.
Hiroko X Kondo, Ryo Kiribayashi, Daisuke Kuroda, Jiro Kohda, Akimitsu Kugimiya, Yu Takano

Sci Rep· December 2019

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Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach.
Hiroko X Kondo, Ayumi Kusaka, Colin K Kitakawa, Jinta Onari, Shusuke Yamanaka, Yu Takano

J Comput Chem· September 2019

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Quantitative Assessment of rPM6 for Fluorine- and Chlorine-Containing Metal Complexes: Comparison with Experimental, First-Principles, and Other Semiempirical Results.
Toru Saito, Manami Fujiwara, Yu Takano

Molecules· December 2018

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Zn-Binding to the Voltage-Gated Proton Channel Hv1/VSOP.
Masayo Iwaki, Kohei Takeshita, Hiroko X Kondo, Kengo Kinoshita, Yasushi Okamura, Yu Takano

J Phys Chem B· October 2018

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Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Takehiko Tosha, Takashi Nomura, Takuma Nishida, Naoya Saeki, Kouta Okubayashi, Takanori Nakane, Yu Takano

Nat Commun· November 2017

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