All
Takada
Brandani
Terakawa
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Molecular mechanism of parental H3/H4 recycling at a replication fork

Nature Communications 15 : 9485

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

Nucleic Acids Research 51 : 5351

ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures

Proceedings of the National Academy of Sciences 119 : e2122523119

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

Biophysics and Physicobiology 19 : e190015

Single-molecule junction spontaneously restored by DNA zipper

Nature Communications 12 : 5762

The lane-switch mechanism for nucleosome repositioning by DNA translocase

Nucleic acids research 49 : 9066

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

PLoS computational biology 17 : e1009265

Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination

Genes & Development 33 : 1191

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

Biophysical journal 116 : 2285

The condensin complex is a mechanochemical motor that translocates along DNA

Science 358 : 672

Sequential eviction of crowded nucleoprotein complexes by the exonuclease RecBCD molecular motor

Proceedings of the National Academy of Sciences 114 : E6322

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

Molecular Simulation 43 : 1315

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

Journal of the American Chemical Society 138 : 8512

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

DNA RECOMBINATION. Base triplet stepping by the Rad51/RecA family of recombinases

Science 349 : 977

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

Biophysical journal 107 : 721

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

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

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

Proceedings of the National Academy of Sciences 109 : 17789

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

Biophysical journal 101 : 1450

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

Journal of computational chemistry 32 : 1228