Publications

2025

• Quantum chemical evaluation of π-π interaction in protein using negative fragmentation approach combined with ONIOM method
  Yu Takano*, Yusuke Kanematsu*, Yuichiro Oda, Hiroko X Kondo, Haruki Nakamura Chemistry Letters 54 upaf099, May 2025

2024

• Quantitative evaluation of noncovalent interactions with negative fragmentation approach including basis set superposition error correction
  Yu Takano*, Hiroko X Kondo, Haruki Nakamura Bulletin of the Chemical Society of Japan 97(9), September 2024
• Structure comparison of heme-binding sites in heme protein predicted by AlphaFold3 and AlphaFold2
  Hiroko X Kondo*, Yu Takano*, Chemistry Letters 53(8), July 2024
• Hydrogen Bond Energies in Helical Peptides Investigated by Negative Fragmentation Approach with Density Functional Theory
  Hiroko X. Kondo, Yu Takano, Seibutsu Butsuri 64(2) 89-93, 2024

2023

• Computational Exploration of Minimum Energy Reaction Pathway of N2O Formation from Intermediate I of P450nor Using an Active Center Model
  Yusuke Kanematsu*, Hiroko X. Kondo, Yu Takano*, International Journal of Molecular Sciences 24(24) 17172-17172, December 2023
• Random Forest Classifier of Heme Proteins Using Porphyrin Distortions and Axial Ligands of Heme
  Hinako Fujikawa, Hiroko X. Kondo, Yusuke Kanematsu, Yu Takano* Chemistry Letters 52(6) 503-507, June 2023
• Negative fragmentation approach for investigating the depolarization effect of neighboring residues on hydrogen bonds in π-helix
  Hiroko X. Kondo*, Haruki Nakamura, Yu Takano* Chemical Physics Letters 815 140361-140361, March 2023
• 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 13(1) 137-137, Janurary 2023

2022

• Quantum chemical studies on hydrogen bonds in helical secondary structures
  Yu Takano, Hiroko X. Kondo, Haruki Nakamura, Biophysical Reviews 14(6) 1369-1378, December 2022
• 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* International Journal of Molecular Sciences 23(24) 15913-15913, December 2022
• Conformational Preference of Flavonols and Its Effect on the Chemical Properties Involved in Radical Scavenging Activity
  Hiroko X. Kondo*, Yu Takano*, Chemistry 4(4) 1123-1135, September 2022
• 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 12(9) 1172-1172, August 2022
• Depolarizing Effects in Hydrogen Bond Energy in 3-10-Helices Revealed by Quantum Chemical Analysis
  Hiroko X. Kondo*, Haruki Nakamura, Yu Takano*, International Journal of Molecular Science 23(16) 9032, August 2022
• Structure of Heme-binding Pocket in Heme Protein is Generally Rigid and can be Predicted by AlphaFold2
  Hiroko X. Kondo*, Yusuke Kanematsu, Yu Takano*, Chemistry Letters 51 704-708, May 2022
• 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*, Journal of Chemical Information and Modeling 62(4) 775-784, February 2022
• Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin
  Hiroko X. Kondo*, Yu Takano, Life 12(2) 210, January 2022

2021

• ヘムタンパク質の機能発現メカニズムの解明に向けたデータベースの整備と機械学習を用いた解析
  近藤 寛子, フロンティア 3(1) 29-36, January 2021

2020

• PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins
  Hiroko X Kondo*, Yusuke Kanematsu*, Gen Masumoto, Yu Takano*, Database 2023 baaa066, October 2020
• Computational study of distortion effect of Fe-porphyrin found as a biological active site
  Yu Takano, Hiroko X. Kondo, Yusuke Kanematsu, Yasuhiro Imada, Japanese Journal of Applied Physics 59(1) 010502, January 2020

2019

• 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, Yasuhisa Nakano, Kouhei Tsumoto, Yu Takano*, Scientific Reports 9(1) 19840, December 2019
• 電位依存性カリウムチャネルKv1.2の変異体における不活性化の分子機構の解析
  近藤寛子, 吉田紀生, 城田松之, アンサンブル 21 283-289, October 2019
• 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, Haruki Nakamura, Yu Takano*, Journal of Computational Chemistry 40 2043-2052, May 2019

2018

• Molecular mechanism of depolarization-dependent inactivation in W366F mutant of Kv1.2
  Hiroko X Kondo, Norio Yoshida, Matsuyuki Shirota, Kengo Kinoshita*, The Journal of Physical Chemistry B 122(48) 10825-10833, November 2018
• Statistical and quantum-chemical analysis of the effect of heme porphyrin distortion in heme proteins: Differences between oxidoreductases and oxygen carrier proteins
  Yusuke Kanematsu*, Hiroko X. Kondo, Yasuhiro Imada, Yu Takano* Chemical Physics Letters 710 108-112, October 2018
• Zn2+-binding to the voltage-gated proton channel Hv1/VSOP
  Masayo Iwaki, Kohei Takeshita, Hiroko X. Kondo, Kengo Kinoshita, Yasushi Okamura, Yu Takano, Atsushi Nakagawa, Hideki Kandori* The Journal of Physical Chemistry B 122 9076-9080, October 2018
• アンキリンが生体膜に相互作用する構造基盤
  藤原 祐一郎, 近藤 寛子, 城田 松之, 木下 賢吾, 生物物理 58(3) 152-154, May 2018
• The evolutionary process of mammalian sex determination genes focusing on marsupial SRYs Yukako Katsura*, Hiroko X. Kondo, Janelle Ryan, Vincent Harley, Yoko Satta, BMC Evolutionary Biology 18 3, January 2018

2011

• Free-Energy Landscapes of Protein Domain Movements upon Ligand Binding
  Hiroko X. Kondo, Noriaki Okimoto*, Gentaro Morimoto, Makoto Taiji, Journal of Physical Chemistry B 115(23) 7629-7636, June 2011