J. Higo

发表

Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes

Haruki Nakamura, J. Higo, Jinzen Ikebe, 2012, Biophysical Reviews.

Multi-scale ensemble modeling of modular proteins with intrinsically disordered linker regions: application to p53.

S. Takada, J. Higo, Tsuyoshi Terakawa, 2014, Biophysical journal.

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.

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 .

Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces

T. Hirokawa, K. Ikeda, K. Tomii, 2008, BMC Structural Biology.

Universal partitioning of the hierarchical fold network of 50-residue segments in proteins

K. Ikeda, K. Tomii, J. Higo, 2009, BMC structural biology.

Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs

K. Ikeda, K. Tomii, J. Higo, 2005, Protein science : a publication of the Protein Society.

Conformational transition states of a β‐hairpin peptide between the ordered and disordered conformations in explicit water

Haruki Nakamura, J. Higo, N. Kamiya, 2002, Protein science : a publication of the Protein Society.

Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH.

J. Higo, K. Sugase, Y. Nishimura, 2016, Biophysical journal.

Molecular Dynamics of a 15-Residue Poly(l-alanine) in Water: Helix Formation and Energetics

T. Yamato, M. Takano, J. Higo, 1999 .

Energy landscape of a peptide consisting of α‐helix, 310‐helix, β‐turn, β‐hairpin, and other disordered conformations

Haruki Nakamura, N. Nakajima, J. Higo, 2001 .

Enhanced conformational diversity search of CDR‐H3 in antibodies: Role of the first CDR‐H3 residue

N. Nakajima, H. Shirai, J. Higo, 1999, Proteins.

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.

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

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

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

T. Kawabata, Y. Fukunishi, Haruki Nakamura, 2020, bioRxiv.

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

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

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

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

Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

J. Higo, K. Umezawa, 2014, Advances in experimental medicine and biology.

A theoretical approach to the bell-shaped dependency of cell proliferation on the hormone concentration.

J. Higo, H. Umeyama, 1997, Journal of theoretical biology.

Calculation of protein-ligand binding free energy using smooth reaction path generation (SRPG) method: a comparison of the explicit water model, gb/sa model and docking score function.

Y. Fukunishi, Haruki Nakamura, J. Higo, 2009, Genome informatics. International Conference on Genome Informatics.

Collective solvent flows around a protein investigated by molecular dynamics simulation.

S. Shimotakahara, J. Higo, K. Umezawa, 2007, The Journal of chemical physics.

Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations

J. Higo, N. Kamiya, I. Fukuda, 2020, Scientific Reports.

Transition state of a SH3 domain detected with principle component analysis and a charge‐neutralized all‐atom protein model

Hironori K. Nakamura, K. Ikeda, J. Higo, 2006, Proteins.

Conformational requirement on peptides to exert laminin's activities and search for protein segments with laminin's activities

Haruki Nakamura, J. Higo, Jinzen Ikebe, 2009, Biopolymers.

Thymine at —5 Is Crucial for cpc Promoter Activity of Synechocystis sp. Strain PCC 6714

T. Hirokawa, J. Higo, M. Imashimizu, 2003, Journal of bacteriology.

Model study of two‐dimensional protein aggregates in the nucleation stage of crystallization

J. Higo, K. Nagayama, 1993 .

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Y. Fukunishi, J. Higo, K. Kasahara, 2022, Biophysical Reviews.

Free‐energy landscape of a chameleon sequence in explicit water and its inherent α/β bifacial property

K. Ikeda, J. Higo, 2003 .

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

Haruki Nakamura, Junichi Higo, Satoshi Ono, 2000 .

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Y. Fukunishi, J. Higo, K. Kasahara, 2022, Biophysical Reviews.

Conformational deformation in deoxymyoglobin by hydrostatic pressure

N. Go, T. Yamato, J. Higo, 1993, Proteins.

Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation

Y. Fukunishi, K. Moritsugu, J. Higo, 2021, J. Chem. Inf. Model..

Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities

T. Kawabata, Y. Fukunishi, Haruki Nakamura, 2021, Scientific Reports.

Modeling of protein loops by simulated annealing

J. Garnier, V. Collura, J. Higo, 1993, Protein science : a publication of the Protein Society.

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.

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..

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.

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..

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

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

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.

β-hairpin folds by molecular dynamics simulations

Haruki Nakamura, O. Galzitskaya, J. Higo, 2000 .

Solvent density and long‐range dipole field around a DNA‐binding protein studied by molecular dynamics

H. Kono, A. Sarai, J. Higo, 2000, Proteins.

Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation.

A. Kidera, N. Nakajima, H. Shirai, 1998, Journal of molecular biology.

Model Building Study of Complex Structures Using NMR Chemical Shift Change Information

A. Heger, Haruki Nakamura, J. Higo, 1997 .

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.

Construction of a T cell receptor signaling range for spontaneous development of autoimmune disease

T. Nomura, D. Standley, R. Ueda, 2022, The Journal of experimental medicine.

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..

Solvent flow patterns fluctuating largely around a protein and correlation with solvent density fluctuations: A molecular dynamics study.

Haruki Nakamura, J. Higo, K. Umezawa, 2010, The Journal of chemical physics.

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

H. Wako, J. Higo, K. Nagayama, 1996, J. Comput. Chem..

Structural refinement by restrained molecular‐dynamics algorithm with small‐angle X‐ray scattering constraints for a biomolecule

J. Higo, M. Kojima, Kenji Takahashi, 2004 .

Intrinsic disorder accelerates dissociation rather than association

M. Takano, J. Higo, J. Ohnuki, 2016, Proteins.

A simulated annealing method for modeling the antigen combining site of antibodies

J. Gibrat, J. Garnier, V. Collura, 1992 .

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

Haruki Nakamura, Akinori Kidera, Junichi Higo, 1997 .

General dynamic properties of Abeta12-36 amyloid peptide involved in Alzheimer's disease from unfolding simulation.

O. Galzitskaya, J. Higo, D. Mitomo, 2004, Journal of biochemistry.

Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

Y. Fukunishi, H. Kono, J. Higo, 2022, Scientific Reports.

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

Shigeru Endo, Toshikazu Ebisuzaki, Tomoyoshi Ito, 1994, 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..

Hydrogen-bond patterns in the hydration structure of a protein

T. Yokomizo, Masayoshi Nakasako, Toshimasa Yamazaki, 2005 .

Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations

J. Higo, N. Kamiya, I. Fukuda, 2020, Scientific Reports.

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.

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

Junichi Higo, Kuniaki Nagayama, Mariko Yamaki, 1995 .

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.

Cyclic peptide analysis of the biologically active loop region in the laminin alpha3 chain LG4 module demonstrates the importance of peptide conformation on biological activity.

A. Utani, J. Higo, K. Umezawa, 2007, Biochemistry.

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

J. Higo, Jinzen Ikebe, K. Umezawa, 2016, Biophysical Reviews.

Virtual states introduced for overcoming entropic barriers in conformational space

Haruki Nakamura, J. Higo, 2012, Biophysics.

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

Haruki Nakamura, Junichi Higo, Narutoshi Kamiya, 2009 .

Free energy landscapes of peptides by enhanced conformational sampling.

A. Kidera, N. Nakajima, J. Higo, 2000, Journal of molecular biology.

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..

Molecular Mechanisms of Functional Modulation of Transcriptional Coactivator PC4 via Phosphorylation on Its Intrinsically Disordered Region

J. Higo, K. Kasahara, Takuya Takahashi, 2023, ACS omega.

Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

Y. Fukunishi, J. Higo, N. Kamiya, 2021, Scientific Reports.

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.

Generalized–ensemble method study: A helix‐mimetic compound inhibits protein–protein interaction by long‐range and short‐range intermolecular interactions

Y. Fukunishi, J. Higo, A. Yoshimori, 2021, J. Comput. Chem..

Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes

Haruki Nakamura, J. Higo, Jinzen Ikebe, 2012, Biophysical Reviews.

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.

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.

Density, Diffusion, and Site-Dipole Field of Solvent around Four Types of Flavonoid Studid by Molecular Dynamics

J. Higo, N. Kamiya, T. Yokomizo, 2008 .

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, Protein science : a publication of the Protein Society.

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..

Molecular dynamics coupled with a virtual system for effective conformational sampling

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

Multi-dimensional virtual system introduced to enhance canonical sampling.

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

Enhancement of canonical sampling by virtual-state transitions.

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

AMBER-based hybrid force field for conformational sampling of polypeptides

Junichi Higo, Narutoshi Kamiya, Satoshi Ono, 2005 .

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

Haruki Nakamura, Junichi Higo, Satoshi Ono, 2000 .

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.

A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins.

J. Higo, K. Ogata, K. Soejima, 2006, Journal of biochemistry.

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

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

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

Haruki Nakamura, Junichi Higo, Satoshi Ono, 1999 .

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..

Protein dynamics determined by backbone conformation and atom packing.

J. Higo, J Higo, H Umeyama, 1997, Protein engineering.

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.

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

Haruki Nakamura, Bhaskar Dasgupta, Junichi Higo, 2016 .

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.

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 .

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 .

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..

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 .

Directional ordering of protein molecules in a two-dimensional hexagonal lattice. An approach with a poker chip model

J. Higo, K. Nagayama, S. Endo, 1992 .

Conformational requirement on peptides to exert laminin's activities and search for protein segments with laminin's activities

Haruki Nakamura, J. Higo, Jinzen Ikebe, 2009, Biopolymers.

Two‐component multicanonical Monte Carlo method for effective conformation sampling

Haruki Nakamura, Akinori Kidera, Junichi Higo, 1997 .

Topographical metric to analyze the thermal fluctuations of protein conformation

T. Yamato, J. Higo, M. Saito, 1994 .

Construction of a T cell receptor signaling range for spontaneous development of autoimmune disease

T. Nomura, D. Standley, R. Ueda, 2022, The Journal of experimental medicine.

Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules

H. Shirai, J. Higo, M. Sasai, 2001, Proceedings of the National Academy of Sciences of the United States of America.