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ORCIDShoji Takada
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2020 – today
- 2023
[j14]Azuki Mizutani, Cheng Tan
, Yuji Sugita, Shoji Takada:
Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study. PLoS Comput. Biol. 19(7) (2023)- 2022
- [j13]Takumi Washio, Xiaoke Cui, Ryo Kanada, Jun-ichi Okada, Seiryo Sugiura, Yasushi Okuno, Shoji Takada, Toshiaki Hisada:
Using incomplete Cholesky factorization to increase the time step in molecular dynamics simulations. J. Comput. Appl. Math. 415: 114519 (2022) - [j12]Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, Yuji Sugita:
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. PLoS Comput. Biol. 18(4) (2022) - 2021
- [j11]Giovanni B. Brandani, Cheng Tan, Shoji Takada:
The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study. PLoS Comput. Biol. 17(7) (2021) - [j10]Hiroki Koide, Noriyuki Kodera, Shveta Bisht, Shoji Takada, Tsuyoshi Terakawa:
Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy. PLoS Comput. Biol. 17(7) (2021) - [j9]Toru Niina, Yasuhiro Matsunaga, Shoji Takada:
Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure. PLoS Comput. Biol. 17(7) (2021)
2010 – 2019
- 2018
- [j8]Giovanni B. Brandani, Shoji Takada:
Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA. PLoS Comput. Biol. 14(11) (2018) - 2017
- [j7]Shintaroh Kubo, Wenfei Li, Shoji Takada:
Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations. PLoS Comput. Biol. 13(9) (2017) - [j6]Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada:
Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations. PLoS Comput. Biol. 13(12) (2017) - 2015
- [j5]Tomohiro Tanaka, Naoto Hori, Shoji Takada:
How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations. PLoS Comput. Biol. 11(7) (2015) - [j4]Hiroo Kenzaki, Shoji Takada:
Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations. PLoS Comput. Biol. 11(8) (2015) - 2013
- [j3]Le Chang, Takeshi Ishikawa, Kazuo Kuwata, Shoji Takada:
Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions. J. Comput. Chem. 34(14): 1251-1257 (2013) - [j2]Ryo Kanada, Takeshi Kuwata, Hiroo Kenzaki, Shoji Takada:
Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin. PLoS Comput. Biol. 9(2) (2013) - 2011
- [j1]Tsuyoshi Terakawa, Tomoshi Kameda, Shoji Takada:
On easy implementation of a variant of the replica exchange with solute tempering in GROMACS. J. Comput. Chem. 32(7): 1228-1234 (2011)
2000 – 2009
- 2005
- [c2]Kazutoshi Fujikawa, Wenzhen Jin, Sung-Joon Park, Tadaomi Furuta, Shoji Takada, Hiroshi Arikawa, Susumu Date, Shinji Shimojo:
Applying a Grid Technology to Protein Structure Predictor "ROKKY". HealthGrid 2005: 27-36 - 2003
- [c1]Seung Yup Lee, Yoshimi Fujitsuka, Shoji Takada, Do Hyun Kim:
What makes IgG binding domain of protein L fold up to native state: a simulation study with physical oriented energy functions coupled to topology induced terms. CSB 2003: 456-457
Coauthor Index
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