Electronic structures of heme a of cytochrome c oxidase in the redox states - Charge density migration to the propionate groups of heme a. - Yu Takano; Haruki Nakamura (J. Comput. Chem., 2010)

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water. - Jinzen Ikebe; Koji Umezawa; Narutoshi Kamiya; Takanori Sugihara; Yasushige Yonezawa; Yu Takano; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2011)

Protein folding pathways extracted by OFLOOD: Outlier FLOODing method. - Ryuhei Harada; Tomotake Nakamura; Yu Takano; Yasuteru Shigeta (J. Comput. Chem., 2015)

Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin. - Ryuhei Harada; Yu Takano; Yasuteru Shigeta (J. Comput. Chem., 2015)

Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile. - Yusuke Kanematsu; Masanori Tachikawa; Yu Takano (J. Comput. Chem., 2016)

Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions. - Yu Takano; Kazuto Nakata; Yasushige Yonezawa; Haruki Nakamura (J. Comput. Chem., 2016)

Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding. - Ryuhei Harada; Yu Takano; Yasuteru Shigeta (J. Comput. Chem., 2017)

Density functional study of porphyrin distortion effects on redox potential of heme. - Yasuhiro Imada; Haruki Nakamura; Yu Takano (J. Comput. Chem., 2018)

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 (J. Comput. Chem., 2019)

PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins. - Hiroko X. Kondo; Yusuke Kanematsu; Gen Masumoto; Yu Takano (Database J. Biol. Databases Curation, 2020)

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., 2022)