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Biophysical Journal|September 28, 2011
Multiscale ensemble modeling of intrinsically disordered proteins: p53 N-terminal domainTsuyoshi Terakawa, Shoji TakadaScientific Reports|November 25, 2015
p53 dynamics upon response element recognition explored by molecular simulationsTsuyoshi Terakawa, Shoji TakadaJournal of Chemical Theory and Computation|November 19, 2015
RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding ProteinsTsuyoshi Terakawa, Shoji TakadaJournal of Computational Chemistry|March 23, 2011
On easy implementation of a variant of the replica exchange with solute tempering in GROMACSTsuyoshi Terakawa, Tomoshi Kameda, Shoji TakadaBiophysical Journal|August 8, 2014
Multi-scale ensemble modeling of modular proteins with intrinsically disordered linker regions: application to p53Tsuyoshi Terakawa, Junichi Higo, Shoji TakadaJournal of the American Chemical Society|August 14, 2012
p53 searches on DNA by rotation-uncoupled sliding at C-terminal tails and restricted hopping of core domainsTsuyoshi Terakawa, Hiroo Kenzaki, Shoji TakadaBiophysics and Physicobiology|July 7, 2022
Coarse-grained molecular dynamics simulations of base-pair mismatch recognition protein MutS sliding along DNAKeisuke Inoue, Shoji Takada, Tsuyoshi TerakawaNucleic Acids Research|May 13, 2023
Histone chaperone Nap1 dismantles an H2A/H2B dimer from a partially unwrapped nucleosomeFritz Nagae, Shoji Takada, Tsuyoshi TerakawaJournal of the American Chemical Society|June 17, 2016
Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular DynamicsCheng Tan, Tsuyoshi Terakawa, Shoji TakadaJournal of Molecular Biology|May 5, 2025
Solution AFM Imaging and Coarse-grained Molecular Modeling of Yeast Condensin Structural Variation Coupled to the ATP Hydrolysis CycleHiroki Koide, Noriyuki Kodera, Shoji Takada, et al.Pageof 13