Shoji Takada

Publication Activity (10 Years)

Years Active: 2017-2023
Publications (10 Years): 14

Top Topics

Molecular Dynamics Simulations

Single Molecule

Circulating Tumor

Top Venues

PLoS computational biology

Journal of chemical theory and computation

The Journal of chemical physics

This page only lists publications with an associated author ORCID identifier.

Publications

Diego Ugarte La Torre, Shoji Takada, Yuji Sugita
Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers. The Journal of chemical physics 159 (7) (2023)
Suguru Kato, Shoji Takada, Sotaro Fuchigami
Particle Smoother to Assimilate Asynchronous Movie Data of High-Speed AFM with MD Simulations. Journal of chemical theory and computation (2023)
Azuki Mizutani, Cheng Tan, Yuji Sugita, Shoji Takada
Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study. PLoS computational biology 19 (7) (2023)
Noriyo Mitome, Shintaroh Kubo, Sumie Ohta, Hikaru Takashima, Yuto Shigefuji, Toru Niina, Shoji Takada
Cooperation among c -subunits of F o F 1 -ATP synthase in rotation-coupled proton translocation. eLife 11 (2022)
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 computational biology 18 (4) (2022)
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 computational biology 17 (7) (2021)
Takumi Washio, Ryo Kanada, Xiaoke Cui, Jun-Ichi Okada, Seiryo Sugiura, Shoji Takada, Toshiaki Hisada
Semi-Implicit Time Integration with Hessian Eigenvalue Corrections for a Larger Time Step in Molecular Dynamics Simulations. Journal of chemical theory and computation 17 (9) (2021)
Diego Ugarte La Torre, Shoji Takada
Modeling lipid-protein interactions for coarse-grained lipid and Cα protein models. The Journal of chemical physics 155 (15) (2021)
Giovanni B Brandani, Cheng Tan, Shoji Takada
The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study. PLoS computational biology 17 (7) (2021)
Diego Ugarte La Torre, Shoji Takada
Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation. The Journal of chemical physics 153 (20) (2021)
Toru Niina, Sotaro Fuchigami, Shoji Takada
Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations. Journal of chemical theory and computation 16 (2) (2020)
Sotaro Fuchigami, Toru Niina, Shoji Takada
Particle Filter Method to Integrate High-Speed Atomic Force Microscopy Measurements with Biomolecular Simulations. Journal of chemical theory and computation 16 (10) (2020)
Giovanni B Brandani, Shoji Takada
Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA. PLoS computational biology 14 (11) (2018)
Shintaroh Kubo, Wenfei Li, Shoji Takada
Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations. PLoS computational biology 13 (9) (2017)