Publications by authors named "Junichi Higo"

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Assessment of RNA Force Fields for Dynamic Docking of Small Molecules Using Multicanonical MD Simulations.
Gert-Jan Bekker, Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya

J Chem Theory Comput· November 2025

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A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.
Junichi Higo, Kota Kasahara, Shun Sakuraba, Gert-Jan Bekker, Narutoshi Kamiya

Biophys Physicobiol· April 2025

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Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations.
Gert-Jan Bekker, Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya

ACS Omega· January 2024

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A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems.
Ikuo Fukuda, Kei Moritsugu, Junichi Higo, Yoshifumi Fukunishi

J Chem Phys· December 2023

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Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics.
Junichi Higo, Gert-Jan Bekker, Narutoshi Kamiya, Ikuo Fukuda, Yoshifumi Fukunishi

Biophys Physicobiol· December 2023

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Molecular Mechanisms of Functional Modulation of Transcriptional Coactivator PC4 via Phosphorylation on Its Intrinsically Disordered Region.
Qilin Xie, Kota Kasahara, Junichi Higo, Takuya Takahashi

ACS Omega· April 2023

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Construction of a T cell receptor signaling range for spontaneous development of autoimmune disease.
Atsushi Tanaka, Shinji Maeda, Takashi Nomura, Mara Anais Llamas-Covarrubias, Satoshi Tanaka, Junichi Higo

J Exp Med· February 2023

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Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles.
Yoshifumi Fukunishi, Junichi Higo, Kota Kasahara

Biophys Rev· December 2022

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Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule.
Junichi Higo, Kota Kasahara, Gert-Jan Bekker, Benson Ma, Shun Sakuraba

Sci Rep· August 2022

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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· May 2021

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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

J Chem Inf Model· April 2021

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Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations.
Gert-Jan Bekker, Ikuo Fukuda, Junichi Higo, Yoshifumi Fukunishi, Narutoshi Kamiya

Sci Rep· March 2021

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Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities.
Tomonori Hayami, Narutoshi Kamiya, Kota Kasahara, Takeshi Kawabata, Jun-Ichi Kurita, Junichi Higo

Sci Rep· March 2021

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GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics.
Junichi Higo, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Itaya Hayato

Biophys Physicobiol· December 2020

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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

J Chem Inf Model· October 2020

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myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling.
Kota Kasahara, Hiroki Terazawa, Hayato Itaya, Satoshi Goto, Haruki Nakamura, Junichi Higo

Biophys Physicobiol· October 2020

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Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations.
Gert-Jan Bekker, Ikuo Fukuda, Junichi Higo, Narutoshi Kamiya

Sci Rep· January 2020

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Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism.
Junichi Higo, Kota Kasahara, Mitsuhito Wada, Bhaskar Dasgupta, Narutoshi Kamiya

Protein Eng Des Sel· December 2019

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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· October 2019

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Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review.
Kota Kasahara, Hiroki Terazawa, Takuya Takahashi, Junichi Higo

Comput Struct Biotechnol J· June 2019

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Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder.
Shinji Iida, Takeshi Kawabata, Kota Kasahara, Haruki Nakamura, Junichi Higo

J Chem Theory Comput· April 2019

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Molecular dynamics coupled with a virtual system for effective conformational sampling.
Tomonori Hayami, Kota Kasahara, Haruki Nakamura, Junichi Higo

J Comput Chem· July 2018

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Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.
Kota Kasahara, Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Haruki Nakamura

Nucleic Acids Res· March 2018

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Multi-dimensional virtual system introduced to enhance canonical sampling.
Junichi Higo, Kota Kasahara, Haruki Nakamura

J Chem Phys· October 2017

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Enhancement of canonical sampling by virtual-state transitions.
Junichi Higo, Kota Kasahara, Bhaskar Dasgupta, Haruki Nakamura

J Chem Phys· January 2017

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