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 (CSB, 2003)

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 (HealthGrid, 2005)

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)

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)

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)

Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations. - Hiroo Kenzaki; Shoji Takada (PLoS Comput. Biol., 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)

Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations. - Shintaroh Kubo; Wenfei Li; Shoji Takada (PLoS Comput. Biol., 2017)

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations. - Toru Niina; Giovanni B. Brandani; Cheng Tan 004; Shoji Takada (PLoS Comput. Biol., 2017)

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA. - Giovanni B. Brandani; Shoji Takada (PLoS Comput. Biol., 2018)

The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study. - Giovanni B. Brandani; Cheng Tan 004; 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)

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)

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)

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. - Cheng Tan 004; Jaewoon Jung; Chigusa Kobayashi; Diego Ugarte La Torre; Shoji Takada; Yuji Sugita (PLoS Comput. Biol., 2022)

Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study. - Azuki Mizutani; Cheng Tan 004; Yuji Sugita; Shoji Takada (PLoS Comput. Biol., 2023)

Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion. - Chenyang Gu; Shoji Takada; Giovanni B. Brandani; Tsuyoshi Terakawa (PLoS Comput. Biol., 2025)