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Takada
Brandani
Terakawa
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Data Assimilation to Integrate High-Speed Atomic Force Microscopy with Biomolecular Simulations: Characterization of Drug Target Functions

Drug Development Supported by Informatics Chapter : 255-272

Nucleosomal DNA unwinding pathway through canonical and non-canonical histone disassembly

Communication Biology 7 : 1144

Theoretical insights into rotary mechanism of MotAB in the bacterial flagellar motor

Biophysical Journal 123 : 3587

Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci

PNAS Nexus 3 : pgae226

Combining contact frequency and histone modification data to tune a coarse-grained chromatin model

Biophysical Journal 123 : 366a

Postsynaptic protein assembly in three and two dimensions studied by mesoscopic simulations

Biophysical Journal 122 : 3395

Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers

The Journal of Chemical Physics 159 : 075101

Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study

PLOS Computational Biology 19 : e1011321

Histone chaperone Nap1 dismantles an H2A/H2B dimer from a partially unwrapped nucleosome

Nucleic Acids Research 51 : 5351

Particle Smoother to Assimilate Asynchronous Movie Data of High-Speed AFM with MD Simulations

Journal of Chemical Theory and Computation 19 : 4678

Removing the parachuting artifact using two-way scanning data in high-speed atomic force microscopy

Biophysics and Physicobiology 20 : e200006

Using incomplete Cholesky factorization to increase the time step in molecular dynamics simulations

Journal of Computational and Applied Mathematics 415 : 114519

Molecular dynamics simulations for the study of chromatin biology

Current Opinion in Structural Biology 77 : 102485

The stoichiometric interaction model for mesoscopic MD simulations of liquid-liquid phase separation

Biophysical Journal 121 : 4382

FO-F1 coupling and symmetry mismatch in ATP synthase resolved in every FO rotation step

Biophysical Journal 122 : 2898

Rotational Mechanism of FO Motor in the F-Type ATP Synthase Driven by the Proton Motive Force

Frontiers in Microbiology 13 : 872565

Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations

Frontiers in Molecular Biosciences 9 : 882989

Coarse-grained molecular dynamics simulations of base-pair mismatch recognition protein MutS sliding along DNA

Biophysics and Physicobiology 19 : e190015

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

PLOS Computational Biology 18 : e1009578

Cooperation among c-subunits of FoF1-ATP synthase in rotation-coupled proton translocation

eLife 11 : e69096

Modeling DNA Opening in the Eukaryotic Transcription Initiation Complexes via Coarse-Grained Models

Frontiers in Molecular Biosciences 8 : 772486

The lane-switch mechanism for nucleosome repositioning by DNA translocase

Nucleic acids research 49 : 9066

Semi-Implicit Time Integration with Hessian Eigenvalue Corrections for a Larger Time Step in Molecular Dynamics Simulations

Journal of Chemical Theory and Computation 17 : 5792

Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo

Nucleic Acids Research 49 : 8642

Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

PLoS computational biology 17 : e1009265

The kinetic landscape of nucleosome assembly: a coarse-grained molecular dynamics study

PLoS computational biology 17 : e1009253

Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure

PLoS Computational Biology 17 : e1009215

Modeling lipid–protein interactions for coarse-grained lipid and Cα protein models

The Journal of Chemical Physics 155 : 155101

Opening of cohesin’s SMC ring is essential for timely DNA replication and DNA loop formation

Cell Reports 35 : 108999

Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model

Proceedings of the National Academy of Sciences 118 : e2024324118

Linker DNA length is a key to tri-nucleosome folding

Journal of Molecular Biology 433 : 166792

Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force Microscopy

Frontiers in Molecular Biosciences 8 : 56

The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA

Nucleic acids research 19 : 10831

Resolving the data asynchronicity in high-speed atomic force microscopy measurement via the Kalman Smoother

Scientific Reports 10 : 18393

Coarse-grained implicit solvent lipid force field with a compatible resolution to the C protein representation

The Journal of Chemical Physics 153 : 205101

Particle Filter Method to Integrate High-Speed Atomic Force Microscopy Measurements with Biomolecular Simulations

Journal of Chemical Theory and Computation 16 : 6609

Nucleosome allostery in pioneer transcription factor binding

Proceedings of the National Academy of Sciences 117 : 20586

Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor

Scientific Reports 10 : 8225

Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor

Scientific Reports 10 : 1

How cytoplasmic dynein couples ATP hydrolysis cycle to diverse stepping motions: kinetic modeling

Biophysical Journal 118 : 1930

Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations

Journal of Chemical Theory and Computation 16 : 1349

Nucleosomes as allosteric scaffolds for genetic regulation

Current Opinion in Structural Biology 62 : 93

Gō model revisited

Biophysics and Physicobiology 16 : 248

Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins

Biophysical journal 116 : 2285

Overcoming the Bottleneck of the Enzymatic Cycle by Steric Frustration

Physical Review Letters 122 : 238102

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

PLoS computational biology 14 : e1006512

Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data

Journal of chemical theory and computation 14 : 3877

Interactions of HP1 Bound to H3K9me3 Dinucleosome by Molecular Simulations and Biochemical Assays

Biophysical journal 114 : 2336

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations

Nucleic acids research 46 : 2788

Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein–DNA Complexes

Journal of chemical theory and computation 14 : 1682

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

PLoS computational biology 13 : e1005880

Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations

PLoS computational biology 13 : e1005748

How one-dimensional diffusion of transcription factors are affected by obstacles: coarse-grained molecular dynamics study

Molecular Simulation 43 : 1315

The structural basis of a high affinity ATP binding ε subunit from a bacterial ATP synthase

PloS one 12 : e0177907

Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights

Proceedings of the National Academy of Sciences 113 : E8021

Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations

Scientific Reports 6 : 34441

Dynamic coupling among protein binding, sliding, and DNA bending revealed by molecular dynamics

Journal of the American Chemical Society 138 : 8512

On the ATP binding site of the ε subunit from bacterial F-type ATP synthases

Biochimica et Biophysica Acta (BBA)-Bioenergetics 1857 : 332

p53 dynamics upon response element recognition explored by molecular simulations

Scientific reports 5 : 17107

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

Accounts of Chemical Research 48 : 3026

Partial unwrapping and histone tail dynamics in nucleosome revealed by coarse-grained molecular simulations

PLoS computational biology 11 : e1004443

How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations

PLoS Comput Biol 11 : e1004356

On the Mg2+ binding site of the ε subunit from bacterial F-type ATP synthases

Biochimica et Biophysica Acta (BBA)-Bioenergetics 1847 : 1101

Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

The Journal of Chemical Physics 142 : 212404

Dimer domain swapping versus monomer folding in apo-myoglobin studied by molecular simulations

Physical Chemistry Chemical Physics 17 : 5006

Applying a grid technology to protein structure predictor "ROKKY".

Studies in health technology and informatics 112 : 27

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

Biophysical journal 107 : 721

Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains

Proceedings of the National Academy of Sciences 111 : 10550

RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins

Journal of Chemical Theory and Computation 10 : 711

Bayesian Parameter Inference by Markov Chain Monte Carlo with Hybrid Fitness Measures: Theory and Test in Apoptosis Signal Transduction Network

PloS one 8 : e74178

ATP hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations

J. Am. Chem. Soc. 135 : 8908

Protein‐specific force field derived from the fragment molecular orbital method can improve protein–ligand binding interactions

Journal of computational chemistry 34 : 1251

Folding Coupled with Assembly in Split Green Fluorescent Proteins Studied by Structure-based Molecular Simulations

The Journal of Physical Chemistry B 117 : 13212

Drug uptake pathways of multidrug transporter AcrB studied by molecular simulations and site-directed mutagenesis experiments

Journal of the American Chemical Society 135 : 7474

Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin

PLoS computational biology 9 : e1002907

p53 searches on DNA by rotation-uncoupled sliding at C-terminal tails and restricted hopping of core domains

Journal of the American Chemical Society 134 : 14555

Coarse-Grained Structure-Based Model for RNA-Protein Complexes Developed by Fluctuation Matching

Journal of Chemical Theory and Computation 8 : 3384

Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

Proceedings of the National Academy of Sciences 109 : 17789

Coarse-grained molecular simulations of large biomolecules

Current opinion in structural biology 22 : 130

Rigor of cell fate decision by variable p53 pulses and roles of cooperative gene expression by p53.

Biophysics 8 : 41

Multiscale ensemble modeling of intrinsically disordered proteins: p53 N-terminal domain

Biophysical journal 101 : 1450

CafeMol: a coarse-grained biomolecular simulator for simulating proteins at work

Journal of Chemical Theory and Computation 7 : 1979

Structural Comparison of F1-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations

Structure 19 : 588

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

Proceedings of the National Academy of Sciences 108 : 3504

On easy implementation of a variant of the replica exchange with solute tempering in GROMACS

Journal of computational chemistry 32 : 1228

Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations

Nature communications 1 : 117

Characterizing Protein Energy Landscape by Self-Learning Multiscale Simulations: Application to a Designed β-Hairpin

Biophysical journal 99 : 3029

Multiscale methods for protein folding simulations

Methods 52 : 106

Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations

Proceedings of the National Academy of Sciences 106 : 18237

Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins

Proceedings of the National Academy of Sciences 106 : 4201

Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously

The Journal of chemical physics 130 : 214108

Folding energy landscape and network dynamics of small globular proteins

Proceedings of the National Academy of Sciences 106 : 73

Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms

Proceedings of the National Academy of Sciences 105 : 11182

In silico chaperonin-like cycle helps folding of proteins for structure prediction

Biophysical journal 94 : 2558

Asymmetry in membrane protein sequence and structure: Glycine outside rule

Journal of molecular biology 377 : 74

Secondary structure provides a template for the folding of nearby polypeptides

Proceedings of the National Academy of Sciences 103 : 17765

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

Proceedings of the National Academy of Sciences 103 : 11844

Folding-based molecular simulations reveal mechanisms of the rotary motor F1–ATPase

Proceedings of the National Academy of Sciences 103 : 5367

Protein Grabs a Ligand by Extending Anchor Residues: Molecular Simulation for Ca2+ Binding to Calmodulin Loop

Biophysical journal 90 : 3043

Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study

Proceedings of the National Academy of Sciences 103 : 3141

SimFold energy function for de novo protein structure prediction: consensus with Rosetta

Proteins 62 : 381

Present and future prospects of protein structure prediction

JOURNAL-JAPANESE SOCIETY FOR ARTIFICIAL INTELLIGENCE 20 : 479

Protein folding mechanisms and energy landscape of src SH3 domain studied by a structure prediction toolbox

Chemical physics 307 : 157

Guiding the search for a protein's maximum rate of folding

Chemical physics 307 : 99

Roles of physical interactions in determining protein‐folding mechanisms: Molecular simulation of protein G and α spectrin SH3

Proteins 55 : 128

Optimizing physical energy functions for protein folding

Proteins 54 : 88

Competition between protein folding and aggregation with molecular chaperones in crowded solutions: insight from mesoscopic simulations

Biophysical journal 85 : 3521

A reversible fragment assembly method for de novo protein structure prediction

The Journal of chemical physics 119 : 6895

How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations

Proceedings of the National Academy of Sciences 100 : 11367

De novo design of foldable proteins with smooth folding funnel: Automated negative design and experimental verification

Structure 11 : 581

Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: dynamics

Physical Review E 66 : 051902

Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: statics

Physical Review E 66 : 031911

On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction

The Journal of chemical physics 116 : 9058

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Gō-like model

Journal of molecular biology 313 : 171

Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach

The Journal of Chemical Physics 114 : 5069

Protein folding simulation with solvent‐induced force field: Folding pathway ensemble of three‐helix‐bundle proteins

Proteins 42 : 85

Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics

The Journal of Chemical Physics 114 : 5082

Simulating folding of helical proteins with coarse grained models

Progress of Theoretical Physics Supplement 138 : 366

Gō-ing for the prediction of protein folding mechanisms

Proceedings of the National Academy of Sciences 96 : 11698

Folding dynamics with nonadditive forces: a simulation study of a designed helical protein and a random heteropolymer

The Journal of chemical physics 110 : 11616

Variational theory for site resolved protein folding free energy surfaces

Physical review letters 81 : 5237

Microscopic theory of critical folding nuclei and reconfiguration activation barriers in folding proteins

The Journal of chemical physics 107 : 9585

Statics, metastable states, and barriers in protein folding: A replica variational approach

Physical Review E 55 : 4562

An elementary mode coupling theory of random heteropolymer dynamics

Proceedings of the National Academy of Sciences 94 : 2318

Glassy dynamics of random heteropolymers

Progress of Theoretical Physics Supplement 126 : 49

Multidimensional tunneling in terms of complex classical mechanics: Wave functions, energy splittings, and decay rates in nonintegrable systems

The Journal of Chemical Physics 104 : 3742

Transfer-matrix approach to tunneling between Kolmogorov-Arnold-Moser tori

Physical Review A 52 : 3546

Effects of vibrational excitation on multidimensional tunneling: General study and proton tunneling in tropolone

The Journal of chemical physics 102 : 3977

WKB Theory of Tunneling between Tori

Progress of Theoretical Physics Supplement 116 : 295

Effects of Potential Energy Surface Topography and Isotope Substitution in Atom-Diatom Chemical Reactions: the CL + H2 and D + H2 Systems

Advances in molecular vibrations and collision dynamics 2 : 245

Constant centrifugal potential approximation for atom–diatom chemical reaction dynamics

The Journal of chemical physics 100 : 4284

Wentzel–Kramers–Brillouin theory of multidimensional tunneling: General theory for energy splitting

The Journal of chemical physics 100 : 98

Reaction dynamics of D+ H2→ DH+ H: Effects of potential energy surface topography and usefulness of the constant centrifugal potential approximation

The Journal of chemical physics 96 : 339