Shoji Takada

According to our database, Shoji Takada authored at least 16 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2023

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

Azuki Mizutani, Cheng Tan, Yuji Sugita, Shoji Takada

PLoS Comput. Biol., 2023

2022

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

Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, Yuji Sugita

PLoS Comput. Biol., 2022

Using incomplete Cholesky factorization to increase the time step in molecular dynamics simulations.

Takumi Washio, Xiaoke Cui, Ryo Kanada, Jun-ichi Okada, Seiryo Sugiura, Yasushi Okuno, Shoji Takada, Toshiaki Hisada

J. Comput. Appl. Math., 2022

2021

Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure.

Toru Niina, Yasuhiro Matsunaga, Shoji Takada

PLoS Comput. Biol., 2021

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

Hiroki Koide, Noriyuki Kodera, Shveta Bisht, Shoji Takada, Tsuyoshi Terakawa

PLoS Comput. Biol., 2021

The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.

Giovanni B. Brandani, Cheng Tan, Shoji Takada

PLoS Comput. Biol., 2021

2018

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA.

Giovanni B. Brandani, Shoji Takada

PLoS Comput. Biol., 2018

2017

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations.

Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada

PLoS Comput. Biol., 2017

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

Shintaroh Kubo, Wenfei Li, Shoji Takada

PLoS Comput. Biol., 2017

2015

How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations.

Tomohiro Tanaka, Naoto Hori, Shoji Takada

PLoS Comput. Biol., 2015

Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations.

Hiroo Kenzaki, Shoji Takada

PLoS Comput. Biol., 2015

2013

Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin.

Ryo Kanada, Takeshi Kuwata, Hiroo Kenzaki, Shoji Takada

PLoS Comput. Biol., 2013

Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions.

Le Chang, Takeshi Ishikawa, Kazuo Kuwata, Shoji Takada

J. Comput. Chem., 2013

2011

On easy implementation of a variant of the replica exchange with solute tempering in GROMACS.

Tsuyoshi Terakawa, Tomoshi Kameda, Shoji Takada

J. Comput. Chem., 2011

2005

Applying a Grid Technology to Protein Structure Predictor "ROKKY".

Kazutoshi Fujikawa, Wenzhen Jin, Sung-Joon Park, Tadaomi Furuta, Shoji Takada, Hiroshi Arikawa, Susumu Date, Shinji Shimojo

Proceedings of the From Grid to Healthgrid, 2005

2003

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.

Seung Yup Lee, Yoshimi Fujitsuka, Shoji Takada, Do Hyun Kim

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003