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Journal 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.Proceedings of the National Academy of Sciences of the United States of America|July 4, 2012
Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knotWenfei Li, Tsuyoshi Terakawa, Wei Wang, et al.Biophysical Journal|June 2, 2019
Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of ProteinsRyo Kanada, Tsuyoshi Terakawa, Hiroo Kenzaki, et al.Plos Computational Biology|April 4, 2025
Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusionChenyang Gu, Shoji Takada, Giovanni B Brandani, et al.Nucleic Acids Research|August 8, 2021
The lane-switch mechanism for nucleosome repositioning by DNA translocaseFritz Nagae, Giovanni B Brandani, Shoji Takada, et al.Elife|April 22, 2026
SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin pathMasataka Yamauchi, Giovanni Bruno Brandani, Tsuyoshi Terakawa, et al.Nature Communications|November 21, 2025
Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicaseFritz Nagae, Yutaka Murata, Masataka Yamauchi, et al.Proceedings of the National Academy of Sciences of the United States of America|July 19, 2017
Sequential eviction of crowded nucleoprotein complexes by the exonuclease RecBCD molecular motorTsuyoshi Terakawa, Sy Redding, Timothy D Silverstein, et al.Plos Computational Biology|July 30, 2021
Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopyHiroki Koide, Noriyuki Kodera, Shveta Bisht, et al.Accounts of Chemical Research|November 18, 2015
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular SimulationsShoji Takada, Ryo Kanada, Cheng Tan, et al.Pageof 3