Shoji Takada

17 papers Journal 15Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion.
PLoS Comput. Biol.
Chenyang Gu, Shoji Takada, Giovanni B. Brandani, Tsuyoshi Terakawa
2023 J jnl
Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study.
PLoS Comput. Biol.
Azuki Mizutani, Cheng Tan, Yuji Sugita, Shoji Takada
2022 J jnl
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.
PLoS Comput. Biol.
Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, Yuji Sugita
2022 J jnl
Using incomplete Cholesky factorization to increase the time step in molecular dynamics simulations.
J. Comput. Appl. Math.
Takumi Washio, Xiaoke Cui, Ryo Kanada, Jun-ichi Okada, Seiryo Sugiura, Yasushi Okuno, Shoji Takada, Toshiaki Hisada
2021 J jnl
Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy.
PLoS Comput. Biol.
Hiroki Koide, Noriyuki Kodera, Shveta Bisht, Shoji Takada, Tsuyoshi Terakawa
2021 J jnl
Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure.
PLoS Comput. Biol.
Toru Niina, Yasuhiro Matsunaga, Shoji Takada
2021 J jnl
The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.
PLoS Comput. Biol.
Giovanni B. Brandani, Cheng Tan, Shoji Takada
2018 J jnl
Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA.
PLoS Comput. Biol.
Giovanni B. Brandani, Shoji Takada
2017 J jnl
Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations.
PLoS Comput. Biol.
Shintaroh Kubo, Wenfei Li, Shoji Takada
2017 J jnl
Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations.
PLoS Comput. Biol.
Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada
2015 J jnl
How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations.
PLoS Comput. Biol.
Tomohiro Tanaka, Naoto Hori, Shoji Takada
2015 J jnl
Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations.
PLoS Comput. Biol.
Hiroo Kenzaki, Shoji Takada
2013 J jnl
Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions.
J. Comput. Chem.
Le Chang, Takeshi Ishikawa, Kazuo Kuwata, Shoji Takada
2013 J jnl
Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin.
PLoS Comput. Biol.
Ryo Kanada, Takeshi Kuwata, Hiroo Kenzaki, Shoji Takada
2011 J jnl
On easy implementation of a variant of the replica exchange with solute tempering in GROMACS.
J. Comput. Chem.
Tsuyoshi Terakawa, Tomoshi Kameda, Shoji Takada
2005 — conf
Applying a Grid Technology to Protein Structure Predictor "ROKKY".
HealthGrid
Kazutoshi Fujikawa, Wenzhen Jin, Sung-Joon Park, Tadaomi Furuta, Shoji Takada, Hiroshi Arikawa, Susumu Date, Shinji Shimojo
2003 — conf
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
Seung Yup Lee, Yoshimi Fujitsuka, Shoji Takada, Do Hyun Kim