Application of a High-Performance, Special-Purpose Computer, GRAPE-2A, to Molecular Dynamics. - Junichi Higo; Shigeru Endo; Kuniaki Nagayama; Tomoyoshi Ito; Toshiyuki Fukushige; Toshikazu Ebisuzaki; Daiichiro Sugimoto; Hiroo Miyagawa; Kunihiro Kitamura; Junichiro Makino (J. Comput. Chem., 1994)

Stability of Two-Dimensional Crystalline Aggregates of a PRotein Studied by Molecular Dynamics. - Junichi Higo; Mariko Yamaki; Michiru Hogyoku; Takuya Takahashi; Shigeru Endo; Kuniaki Nagayama (J. Comput. Chem., 1994)

New implementation of and the modeling by the extended simulated annealing process to structures of T4 lysozyme mutants at the 86th residue. - Shigeru Endo; Junichi Higo; Kuniaki Nagayama; Hiroshi Wako (J. Comput. Chem., 1996)

Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95. - Satoshi Ono; Nobuyuki Nakajima; Junichi Higo; Haruki Nakamura (J. Comput. Chem., 2000)

Collective motions of myosin head derived from backbone molecular dynamics and combination with X-ray solution scattering data. - Junichi Higo; Yasunobu Sugimoto; Katsuzo Wakabayashi; Haruki Nakamura (J. Comput. Chem., 2001)

Repeated-annealing sampling combined with multicanonical algorithm for conformational sampling of bio-molecules. - Narutoshi Kamiya; Junichi Higo (J. Comput. Chem., 2001)

Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: On the correlation between crystal water sites, solvent density, and solvent dipole. - Junichi Higo; Masayoshi Nakasako (J. Comput. Chem., 2002)

Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations. - Satoshi Ono; Masataka Kuroda; Junichi Higo; Nobuyuki Nakajima; Haruki Nakamura (J. Comput. Chem., 2002)

Molecular dynamics simulation using coarse-grained model to study protein function and beyond. - Mitsunori Takano; Hironori K. Nakamura; Junichi Higo; Masaki Sasai (IEEE Congress on Evolutionary Computation, 2003)

beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain. - Kazuyoshi Ikeda; Oxana V. Galzitskaya; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2003)

On the model granularity to simulate protein dynamics: A biological physics view on biomolecular computing. - Mitsunori Takano; Junichi Higo; Hironori K. Nakamura; Masaki Sasai (Nat. Comput., 2004)

Sampling of Protein Conformations with Computers to Predict the Native Structure. - Junichi Higo (ISHPC, 2005)

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)

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. - Junichi Higo; Bhaskar Dasgupta; Tadaaki Mashimo; Kota Kasahara; Yoshifumi Fukunishi; Haruki Nakamura (J. Comput. Chem., 2015)

Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method. - Hung Nguyen; Tien Tran; Yoshifumi Fukunishi; Junichi Higo; Haruki Nakamura; Ly Le (J. Chem. Inf. Model., 2015)

Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling. - Shinji Iida; Tadaaki Mashimo; Takashi Kurosawa; Hironobu Hojo; Hiroya Muta; Yuji Goto; Yoshifumi Fukunishi; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2016)

Molecular dynamics coupled with a virtual system for effective conformational sampling. - Tomonori Hayami; Kota Kasahara; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2018)

Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly. - Tomonori Hayami; Junichi Higo; Haruki Nakamura; Kota Kasahara (J. Comput. Chem., 2019)

Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. - Junichi Higo; Takeshi Kawabata; Ayumi Kusaka; Kota Kasahara; Narutoshi Kamiya; Ikuo Fukuda; Kentaro Mori; Yutaka Hata; Yoshifumi Fukunishi; Haruki Nakamura (J. Chem. Inf. Model., 2020)

Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. - Junichi Higo; Hajime Takashima; Yoshifumi Fukunishi; Atsushi Yoshimori (J. Comput. Chem., 2021)

Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation. - Kei Moritsugu; Koh Takeuchi; Narutoshi Kamiya; Junichi Higo; Isao Yasumatsu; Yoshifumi Fukunishi; Ikuo Fukuda (J. Chem. Inf. Model., 2021)