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

Li, Wenfei ; Wolynes, Peter G ; Takada, Shoji

Proceedings of the National Academy of Sciences - PNAS, 2011-03, Vol.108 (9), p.3504-3509 [Periódico revisado por pares]

United States: National Academy of Sciences

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2
Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy
Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy
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Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

Koide, Hiroki ; Kodera, Noriyuki ; Bisht, Shveta ; Takada, Shoji ; Terakawa, Tsuyoshi MacKerell, Alexander

PLoS computational biology, 2021-07, Vol.17 (7), p.e1009265-e1009265 [Periódico revisado por pares]

United States: Public Library of Science

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3
Nucleosome allostery in pioneer transcription factor binding
Nucleosome allostery in pioneer transcription factor binding
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Nucleosome allostery in pioneer transcription factor binding

Tan, Cheng ; Takada, Shoji

Proceedings of the National Academy of Sciences - PNAS, 2020-08, Vol.117 (34), p.20586-20596 [Periódico revisado por pares]

United States: National Academy of Sciences

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4
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations
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Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

Takada, Shoji ; Kanada, Ryo ; Tan, Cheng ; Terakawa, Tsuyoshi ; Li, Wenfei ; Kenzaki, Hiroo

Accounts of chemical research, 2015-12, Vol.48 (12), p.3026-3035 [Periódico revisado por pares]

United States: American Chemical Society

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5
Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study
Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study
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Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study

Mizutani, Azuki ; Tan, Cheng ; Sugita, Yuji ; Takada, Shoji Zhang, Shihua

PLoS computational biology, 2023-07, Vol.19 (7), p.e1011321-e1011321 [Periódico revisado por pares]

United States: Public Library of Science

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6
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
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Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

Tan, Cheng ; Jung, Jaewoon ; Kobayashi, Chigusa ; Torre, Diego Ugarte La ; Takada, Shoji ; Sugita, Yuji Schneidman-Duhovny, Dina

PLoS computational biology, 2022-04, Vol.18 (4), p.e1009578-e1009578 [Periódico revisado por pares]

United States: Public Library of Science

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7
Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains
Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains
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Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains

Li, Wenfei ; Wang, Wei ; Takada, Shoji

Proceedings of the National Academy of Sciences - PNAS, 2014-07, Vol.111 (29), p.10550-10555 [Periódico revisado por pares]

United States: National Academy of Sciences

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8
Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations
Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations
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Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations

Kubo, Shintaroh ; Li, Wenfei ; Takada, Shoji Weinstein, Harel

PLoS computational biology, 2017-09, Vol.13 (9), p.e1005748 [Periódico revisado por pares]

United States: Public Library of Science

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9
Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor
Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor
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Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor

Kubo, Shintaroh ; Niina, Toru ; Takada, Shoji

Scientific reports, 2020-05, Vol.10 (1), p.8225-8225, Article 8225 [Periódico revisado por pares]

London: Nature Publishing Group

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10
Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations
Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations
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Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations

Niina, Toru ; Fuchigami, Sotaro ; Takada, Shoji

Journal of chemical theory and computation, 2020-02, Vol.16 (2), p.1349-1358 [Periódico revisado por pares]

United States: American Chemical Society

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