Junichi Higo

发表

Molecular dynamics coupled with a virtual system for effective conformational sampling

Haruki Nakamura, Kota Kasahara, Tomonori Hayami, 2018, J. Comput. Chem..

Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

Haruki Nakamura, Satoshi Ono, Junichi Higo, 2000, J. Comput. Chem..

Repeated‐annealing sampling combined with multicanonical algorithm for conformational sampling of bio‐molecules

Junichi Higo, Narutoshi Kamiya, J. Higo, 2001, J. Comput. Chem..

Multidimensional virtual‐system coupled canonical molecular dynamics to compute free‐energy landscapes of peptide multimer assembly

Haruki Nakamura, Kota Kasahara, Tomonori Hayami, 2019, J. Comput. Chem..

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water

Haruki Nakamura, Junichi Higo, Narutoshi Kamiya, 2011, J. Comput. Chem..

Virtual‐system‐coupled adaptive umbrella sampling to compute free‐energy landscape for flexible molecular docking

Haruki Nakamura, Kota Kasahara, Bhaskar Dasgupta, 2015, J. Comput. Chem..

Calibration of force‐field dependency in free energy landscapes of peptide conformations by quantum chemical calculations

Haruki Nakamura, Satoshi Ono, Junichi Higo, 2002, J. Comput. Chem..

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme

Haruki Nakamura, Kota Kasahara, Yutaka Akiyama, 2016, Biophysics and physicobiology.

Sampling of Protein Conformations with Computers to Predict the Native Structure

Junichi Higo, 2005, ISHPC.

Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit water

Haruki Nakamura, Junichi Higo, Narutoshi Kamiya, 2009 .

Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling.

Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya, 2020, Journal of chemical information and modeling.

Parallelization of Markov Chain Generation and its Application to the Multicanonical Method

Haruki Nakamura, Junichi Higo, Takanori Sugihara, 2009 .

Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method

Haruki Nakamura, Ly Le, Hung Nguyen, 2015, J. Chem. Inf. Model..

On the model granularity to simulate protein dynamics: A biological physics view on biomolecular computing

Mitsunori Takano, Masaki Sasai, Junichi Higo, 2004, Natural Computing.

Docking simulation with multicanonical WHAM method

Junichi Higo, S. Ono, N. Nakajima, 2000 .

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. Higo, 2002, J. Comput. Chem..

High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations

Haruki Nakamura, Kenji Mizuguchi, Junichi Higo, 2014, Proteins.

New implementation of and the modeling by the extended simulated annealing process to structures of T4 lysozyme mutants at the 86th residue

Hiroshi Wako, Shigeru Endo, Junichi Higo, 1996, J. Comput. Chem..

Stability of two‐dimensional crystalline aggregates of a protein studied by molecular dynamics

Shigeru Endo, Takuya Takahashi, Junichi Higo, 1994, J. Comput. Chem..

Flexible binding simulation by a novel and improved version of virtual-system coupled adaptive umbrella sampling

Haruki Nakamura, Bhaskar Dasgupta, Junichi Higo, 2016 .

Application of a high‐performance, special‐purpose computer, GRAPE‐2A, to molecular dynamics

Shigeru Endo, Toshikazu Ebisuzaki, Tomoyoshi Ito, 1994, J. Comput. Chem..

2P-009 Identification of essential structural variables for medium-size protein-segment and application to structural class assignment(The 46th Annual Meeting of the Biophysical Society of Japan)

Junichi Higo, Kentaro Tomii, Kazuyoshi Ikeda, 2008 .

β‐Hairpins, α‐helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β‐hairpin of SH3 domain

Haruki Nakamura, Oxana V. Galzitskaya, Junichi Higo, 2003, J. Comput. Chem..

myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling

Haruki Nakamura, Satoshi Goto, Takuya Takahashi, 2020, Biophysics and physicobiology.

Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling

Haruki Nakamura, Yoshifumi Fukunishi, Junichi Higo, 2016, J. Comput. Chem..

Enhanced sampling simulations to construct free-energy landscape of protein–partner substrate interaction

Junichi Higo, Jinzen Ikebe, Koji Umezawa, 2015, Biophysical Reviews.

Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review

Junichi Higo, Kota Kasahara, Hiroki Terazawa, 2019, Computational and structural biotechnology journal.

Molecular dynamics study on mobility and dipole ordering of solvent around proteins: effects of periodic-box size and protein charge

Haruki Nakamura, Junichi Higo, Hiroki Shirai, 1999 .

Rotational motions of solvent site–dipole field around a protein

Junichi Higo, Shin Yagihara, Tsuyoshi Yokomizo, 2003 .

Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation

Haruki Nakamura, Akinori Kidera, Junichi Higo, 1997 .

Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations

Junichi Higo, Kota Kasahara, Takuya Takahashi, 2019, PeerJ Physical Chemistry.

Protein‐inhibitor flexible docking by a multicanonical sampling: Native complex structure with the lowest free energy and a free‐energy barrier distinguishing the native complex from the others

Haruki Nakamura, Junichi Higo, Narutoshi Kamiya, 2007, Proteins.

The multicanonical weighted histogram analysis method for the free-energy landscape along structural transition paths

Haruki Nakamura, Junichi Higo, Satoshi Ono, 1999 .

DNA-protein binding mediated by a solvent site-dipole field

Junichi Higo, Hiroo Miyagawa, Nobuyuki Hamasaki, 2006 .

Explicit and GB/SA solvents: Each with two different force fields in multicanonical conformational sampling of a 25-residue polypeptide

Junichi Higo, Narutoshi Kamiya, J. Higo, 2006 .

Two‐component multicanonical Monte Carlo method for effective conformation sampling

Haruki Nakamura, Akinori Kidera, Junichi Higo, 1997 .

Peptide free‐energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

Haruki Nakamura, Junichi Higo, Satoshi Ono, 2000 .

Simulation study on the disordered state of an Alzheimer's β amyloid peptide Aβ(12–36) in water consisting of random‐structural, β‐structural, and helical clusters

Junichi Higo, Narutoshi Kamiya, Jinzen Ikebe, 2007 .

Formulation of Static and Dynamic Conformational Energy Analysis of Biopolymer Systems Consisting of Two or More Molecules–Avoiding a Singularity in the Previous Method

Junichi Higo, Nobuhiro Go, Yasunobu Seno, 1985 .

A virtual-system coupled multicanonical molecular dynamics simulation: principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent.

Haruki Nakamura, Junichi Higo, Haruki Nakamura, 2013, The Journal of chemical physics.

Multi-dimensional virtual system introduced to enhance canonical sampling.

Haruki Nakamura, Junichi Higo, Kota Kasahara, 2017, The Journal of chemical physics.

Ab initio simulation of a 57‐residue protein in explicit solvent reproduces the native conformation in the lowest free‐energy cluster

Haruki Nakamura, Junichi Higo, Jinzen Ikebe, 2011, Protein science : a publication of the Protein Society.

α-Helix and β-Hairpin Folding from Experiment, Analytical Theory and Molecular Dynamics Simulations

Oxana V. Galzitskaya, Junichi Higo, Alexei V. Finkelstein, 2002 .

Conformational sampling of a 40-residue protein consisting of α and β secondary-structure elements in explicit solvent

Haruki Nakamura, Junichi Higo, Narutoshi Kamiya, 2007 .

Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state

Haruki Nakamura, Junichi Higo, Kazuhiro Ogata, 2018, Nucleic acids research.

A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations.

Haruki Nakamura, Junichi Higo, Haruki Nakamura, 2011, Journal of the American Chemical Society.

Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins

Jean Garnier, Junichi Higo, Vincent Collura, 1992, Biopolymers.

Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder.

Takeshi Kawabata, Haruki Nakamura, Junichi Higo, 2019, Journal of chemical theory and computation.

Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism

Haruki Nakamura, Mitsuhito Wada, Yoshifumi Fukunishi, 2019, Protein engineering, design & selection : PEDS.

Enhancement of canonical sampling by virtual-state transitions.

Haruki Nakamura, Junichi Higo, Bhaskar Dasgupta, 2017, The Journal of chemical physics.

Size-Dependent Separation of Colloidal Particles In Two-Dimensional Convective Self-Assembly

Junichi Higo, Kuniaki Nagayama, Mariko Yamaki, 1995 .

Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics

Haruki Nakamura, Mitsunori Takano, Junichi Higo, 2012, Biomolecules.

GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics.

Kentaro Mori, Yoshifumi Fukunishi, Junichi Higo, 2020, Biophysics and physicobiology.

Folding of the 25 residue Abeta(12-36) peptide in TFE/water: temperature-dependent transition from a funneled free-energy landscape to a rugged one.

Joan-Emma Shea, Junichi Higo, Narutoshi Kamiya, 2007, The journal of physical chemistry. B.

The Multicanonical Weighted Histogram Analysis Method for the Free Energy Landscape along Structural Transition Paths

Haruki Nakamura, Junichi Higo, Satoshi Ono, 2000 .

Structure dependency of a 24-residue peptide humanin on solvent and preferential solvation by trifluoroethanol studied by multicanonical sampling

Junichi Higo, Narutoshi Kamiya, Jinzen Ikebe, 2008 .

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation

Haruki Nakamura, Junichi Higo, Haruki Nakamura, 2016, The Biochemical journal.

AMBER-based hybrid force field for conformational sampling of polypeptides

Junichi Higo, Narutoshi Kamiya, Satoshi Ono, 2005 .