N. Kamiya

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.

Molecular Dynamics Simulations of Double-Stranded DNA in an Explicit Solvent Model with the Zero-Dipole Summation Method

Haruki Nakamura, Narutoshi Kamiya, Ikuo Fukuda, 2013, PloS one.

Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water.

Haruki Nakamura, Narutoshi Kamiya, Yasushige Yonezawa, 2012, The Journal of chemical physics.

Application of zero-dipole summation method to molecular dynamics simulations of a membrane protein system

Haruki Nakamura, N. Kamiya, I. Fukuda, 2013 .

Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions.

Haruki Nakamura, Yoshifumi Fukunishi, Narutoshi Kamiya, 2013, Journal of chemical theory and computation.

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 .

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.

Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd3+

N. Kunishima, K. Morikawa, N. Kamiya, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Revisiting antibody modeling assessment for CDR-H3 loop

Haruki Nakamura, N. Kamiya, H. Nishigami, 2016, Protein engineering, design & selection : PEDS.

Thermal stability of single‐domain antibodies estimated by molecular dynamics simulations

N. Kamiya, G. Bekker, Benson Ma, 2018, Protein science : a publication of the Protein Society.

In silico prediction of the chemical block of human ether-a-go-go-related gene (hERG) K+ current.

Haruki Nakamura, Yoshifumi Fukunishi, Narutoshi Kamiya, 2008, The journal of physiological sciences : JPS.

Mutational Analysis of Block and Facilitation of HERG Current by A Class III Anti-Arrhythmic Agent, Nifekalant

K. Kinoshita, Y. Fukunishi, Haruki Nakamura, 2007, Channels.

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.

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

B. Dasgupta, Haruki Nakamura, A. Kinjo, 2014, PloS one.

Rational discovery of a novel interface for a coactivator in the peroxisome proliferator‐activated receptor γ: Theoretical implications of impairment in type 2 diabetes mellitus

N. Kamiya, T. Kodama, H. Jingami, 2004, Proteins.

Structural and thermodynamic characterization of endo-1,3-β-glucanase: Insights into the substrate recognition mechanism.

B. Mikami, M. Oda, N. Kamiya, 2018, Biochimica et biophysica acta. Proteins and proteomics.

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

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

Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

Y. Okuno, N. Kamiya, G. Bekker, 2020, Nature Communications.

Metal binding to cutinase-like enzyme from Saccharomonospora viridis AHK190 and its effects on enzyme activity and stability.

M. Oda, N. Kamiya, G. Bekker, 2019, Journal of biochemistry.

Alpha,beta-unsaturated ketone is a core moiety of natural ligands for covalent binding to peroxisome proliferator-activated receptor gamma.

N. Kamiya, T. Kodama, H. Jingami, 2005, The Journal of biological chemistry.

Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking

N. Kamiya, G. Bekker, 2022, Biophysical Reviews.

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..

SUB-PICOSECOND FLUORESCENCE SPECTROSCOPY OF THE M INTERMEDIATE IN THE PHOTOCYCLE OF BACTERIORHODOPSIN BY USING UP-CONVERSION FLUOROMETRY

Takayoshi Kobayashi, N. Kamiya, T. Sekikawa, 1999 .

Picosecond-millisecond dual-time-base spectroscopy of fluorescent photointermediates formed in the purple membrane of Halobacterium halobium

N. Kamiya, M. Ishikawa, H. Ohtani, 1999 .

Picosecond fluorescence spectroscopy of the purple membrane of Halobacterium halobium in alkaline suspension

N. Kamiya, M. Ishikawa, H. Ohtani, 1997 .

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.

Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor.

Haruki Nakamura, Yasushi Okuno, Mitsugu Araki, 2017, Journal of chemical theory and computation.

Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids.

K. Morikawa, N. Kamiya, H. Jingami, 2009, Journal of molecular biology.

Application of MDGRAPE‐3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems

Haruki Nakamura, Ryutaro Himeno, Makoto Taiji, 2009, J. Comput. Chem..

α,β-Unsaturated Ketone Is a Core Moiety of Natural Ligands for Covalent Binding to Peroxisome Proliferator-activated Receptor γ*

N. Kamiya, T. Kodama, H. Jingami, 2005, Journal of Biological Chemistry.

Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability

M. Oda, N. Ito, N. Kamiya, 2020, Proteins.

Computational analysis of ligand recognition mechanisms by prostaglandin E2 (subtype 2) and D2 receptors

T. Hirokawa, H. Toh, H. Daiyasu, 2011 .

NMR Characterization of the Interaction of the Endonuclease Domain of MutL with Divalent Metal Ions and ATP

N. Kamiya, K. Fukui, Y. Takano, 2014, PloS one.

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.

Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle.

M. Oda, N. Ito, N. Kamiya, 2018, Biochemistry.

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..

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

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

Model Building of Antibody-Antigen Complex Structures Using GBSA Scores

Haruki Nakamura, Narutoshi Kamiya, Noriko Shimba, 2016, J. Chem. Inf. Model..

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.

Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations

Genji Kurisu, Haruki Nakamura, Narutoshi Kamiya, 2016, Protein engineering, design & selection : PEDS.

Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns

Biao Ma, Yasushi Okuno, Kei Terayama, 2020, J. Chem. Inf. Model..

Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations.

Yasushi Okuno, Mitsugu Araki, Narutoshi Kamiya, 2019, The journal of physical chemistry. B.

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

Haruki Nakamura, Junichi Higo, Narutoshi Kamiya, 2009 .

Folding thermodynamics of PET-hydrolyzing enzyme Cut190 depending on Ca2+ concentration

M. Oda, N. Kamiya, G. Bekker, 2018, Journal of Thermal Analysis and Calorimetry.

Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL

N. Kamiya, G. Bekker, M. Araki, 2023, Communications Biology.

N-Terminal-Driven Binding Mechanism of an Antigen Peptide to Human Leukocyte Antigen-A*2402 Elucidated by Multicanonical Molecular Dynamic-Based Dynamic Docking and Path Sampling Simulations.

N. Kamiya, G. Bekker, 2021, The journal of physical chemistry. B.

Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking

Yasushi Okuno, Mitsugu Araki, Narutoshi Kamiya, 2021, J. Chem. Inf. Model..

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.

Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Mitsugu Araki, Narutoshi Kamiya, Gert-Jan Bekker, 2020, J. Comput. Chem..

Structure of the entire stalk region of the Dynein motor domain.

Genji Kurisu, Haruki Nakamura, Narutoshi Kamiya, 2014, Journal of molecular biology.

Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level.

N. Kamiya, G. Bekker, 2021, Methods in molecular biology.

Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization.

M. Oda, N. Kamiya, G. Bekker, 2021, Methods in enzymology.

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.

The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems.

Haruki Nakamura, Narutoshi Kamiya, Ikuo Fukuda, 2014, The Journal of chemical physics.

Effects of hydration on the electronic structure of an enzyme: implications for the catalytic function.

Y. Inoue, M. Sakurai, N. Kamiya, 2001, Journal of the American Chemical Society.

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 .

AMBER-based hybrid force field for conformational sampling of polypeptides

Junichi Higo, Narutoshi Kamiya, Satoshi Ono, 2005 .

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

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

Improving the Accuracy of Protein‐Ligand Binding Mode Prediction Using a Molecular Dynamics‐Based Pocket Generation Approach

Koji Tsuda, Biao Ma, Hiroaki Iwata, 2018, J. Comput. Chem..

Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method.

Haruki Nakamura, Narutoshi Kamiya, Yasushige Yonezawa, 2011, Journal of chemical theory and computation.

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 .

Dynamical Methods to Study Interaction in Proteins Facilitating Molecular Understanding of Cancer

B. Dasgupta, N. Kamiya, G. Bekker, 2021, Handbook of Oxidative Stress in Cancer: Mechanistic Aspects.

Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02

N. Kamiya, G. Bekker, Maki Kawasaki, 2023, Protein science : a publication of the Protein Society.

Structure of the entire stalk region of the Dynein motor domain.

Haruki Nakamura, Y. Toyoshima, N. Kamiya, 2014, Journal of molecular biology.

The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors

Masahiko Nakatsui, Takatsugu Hirokawa, Yasushi Okuno, 2016, J. Chem. Inf. Model..