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List of works by Akio Kitao

An Efficient Timer and Sizer of Biomacromolecular Motions

scientific article published on 25 November 2019

Binding free energy analysis of protein-protein docking model structures by evERdock.

scientific article published in March 2018

Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra

scientific article published on 29 November 2019

ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation

scientific article published on 11 July 2018

Collective dynamics of periplasmic glutamine binding protein upon domain closure

scientific article published on November 2009

Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space

scientific article published in October 1994

Computational analysis of thermal stability: effect of Ile-->Val mutations in human lysozyme.

scientific article published in January 1998

CyClus: a fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys

scientific article published on 27 February 2013

DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins

scientific article

Design, synthesis and structure-activity relationship studies of novel sirtuin 2 (SIRT2) inhibitors with a benzamide skeleton

scientific article published on 02 December 2014

Detecting coupled collective motions in protein by independent subspace analysis.

scientific article published in November 2010

Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model

scientific article published on 30 January 2019

Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes

scientific article

Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins

scientific article published on 01 June 2020

Effect of solvent on collective motions in globular protein.

scientific article published in December 1993

Effects of water model and simulation box size on protein diffusional motions.

scientific article published on 21 September 2007

Energy landscape of a native protein: jumping-among-minima model

scientific article published on 01 December 1998

Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding.

scientific article

Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method

scientific article published on 19 August 2019

Eritoran inhibits S100A8-mediated TLR4/MD-2 activation and tumor growth by changing the immune microenvironment.

scientific article published on 13 July 2015

Erratum: "Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins" [J. Chem. Phys. 152, 225101 (2020)]

scientific article published on 01 November 2020

Essential ion binding residues for Na+ flow in stator complex of the Vibrio flagellar motor

scientific article published on 02 August 2019

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

scientific article published on 01 December 2012

Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method

scientific article published on 22 June 2011

Functional Conversion of CPD and (6-4) Photolyases by Mutation

scientific article

Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor

scientific article published on 8 June 2015

Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility

scientific article published on 23 April 2019

Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis ⬇️

scientific article published on June 1, 1994

Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis

scientific article published on 01 October 1995

High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments

scientific article

High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration

scientific article published on 11 February 2020

High quality rendering of protein dynamics in space filling mode

scientific article

How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme ⬇️

scientific article published on September 1, 2003

Hydration affects both harmonic and anharmonic nature of protein dynamics

scientific article

Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra.

scientific article published on 29 February 2008

Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline staphylococcal nuclease

scientific article published on 23 February 2008

Impact of key residues within chloroplast thioredoxin-f on recognition for reduction and oxidation of target proteins

scientific article published on 09 October 2019

Improved protein free energy calculation by more accurate treatment of nonbonded energy: application to chymotrypsin inhibitor 2, V57A.

scientific article published in March 1998

Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins

scientific article

Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding

scientific article published on 01 April 2020

Mechanical unfolding of bacterial flagellar filament protein by molecular dynamics simulation.

scientific article published on 4 December 2009

Mechanism of deep-sea fish α-actin pressure tolerance investigated by molecular dynamics simulations

scientific article published on 20 January 2014

Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme

scientific article published on 01 March 1997

Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic β-Proline Oligomers: Length-Dependent Convergence to Organized Structures.

scientific article

Molecular dynamics simulation of bacterial flagella

scientific article published on 27 November 2017

Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics

scientific article published on 11 July 2019

Molecular dynamics simulation shows large volume fluctuations of proteins

scientific article published on 01 January 2000

Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase

scientific article

Monte Carlo Sampling with Linear Inverse Kinematics for Simulation of Protein Flexible Regions

scientific article published on 01 August 2015

More efficient screening of protein-protein complex model structures for reducing the number of candidates

scientific article published on 29 November 2019

MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.

scientific article published in October 2013

Multi-strand β-sheet of Alzheimer Aβ(1-40) folds to β-strip helix: Implication for protofilament formation

scientific article published on 07 December 2018

Multidimensional replica-exchange method for free-energy calculations

Multiple Markov transition matrix method: obtaining the stationary probability distribution from multiple simulations

scientific article

Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation

scientific article published on 24 April 2007

Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins

scientific article published on 21 October 2015

Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation

scientific article published on 3 January 2018

Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7

scientific article published on 18 October 2019

Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation

scholarly article

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

scientific article published in 2009

Protein boson peak originated from hydration-related multiple minima energy landscape

scientific article published on 01 June 2005

Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics

scientific article published on 28 November 2017

Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations

scientific article published on 01 November 2018

Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature.

scientific article published on 28 July 2017

Screw motion regulates multiple functions of T4 phage protein gene product 5 during cell puncturing.

scientific article

Similarities and Differences between Thymine(6-4)Thymine/Cytosine DNA Lesion Repairs by Photolyases

scientific article published on 30 August 2018

Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus

scientific article published on 25 April 2019

Structure of the MotA/B Proton Channel.

scientific article published in January 2017

Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism

scientific article published in October 2004

Structure of the cytoplasmic domain of FlhA and implication for flagellar type III protein export

scientific article

Switch interactions control energy frustration and multiple flagellar filament structures

scientific article

TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P₂

scientific article

The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing

scientific article published on 22 December 2011

The effect of end constraints on protein loop kinematics

scientific article published on May 2010

Thermal unfolding simulations of bacterial flagellin: insight into its refolding before assembly.

scientific article published on 8 February 2008

Transform and relax sampling for highly anisotropic systems: application to protein domain motion and folding

scientific article published on July 2011

Universality and Structural Implications of the Boson Peak in Proteins

scientific article published on 14 June 2019

Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins

scientific article published on 23 May 2018

Water model tuning for improved reproduction of rotational diffusion and NMR spectral density.

scientific article

[Protein energy landscape and dynamics studied by molecular simulations and neutron scattering]

scientific article published on 01 July 2006

[Structure, function and self-assembly of the bacterial flagellum].

scientific article published in August 2005

[Universal joint of biological supramolecule: mechanism of bacterial flagellar hook investigated in silico]

scientific article published on 01 August 2005

evERdock BAI: Machine-learning-guided selection of protein-protein complex structure

scientific article published on 01 December 2019

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