Shoji Takada

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 9

Top Topics

Atomic Force Microscopy

Simulation Study

Top Venues

PLoS Comput. Biol.

J. Comput. Appl. Math.

J. Comput. Chem.

Publications

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)
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)
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 (2022)
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)
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)
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)
Giovanni B. Brandani, Shoji Takada
Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA. PLoS Comput. Biol. 14 (11) (2018)
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)
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)
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)
Hiroo Kenzaki, Shoji Takada
Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations. PLoS Comput. Biol. 11 (8) (2015)
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)
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) (2013)
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) (2011)
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)
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)