Takashi Yoshidome
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Explore the profile of Takashi Yoshidome including associated specialties, affiliations and a list of published articles.
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Articles
29
Citations
134
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Recent Articles
1.
Yoshidome T
J Comput Chem
. 2023 Dec;
45(11):738-751.
PMID: 38112413
Elucidating protein conformational changes is essential because conformational changes are closely related to the functions of proteins. Cryo-electron microscopy (cryo-EM) experiment can be used to reconstruct protein conformational changes via...
2.
Hishikawa Y, Noya H, Nagatoishi S, Yoshidome T, Maity B, Tsumoto K, et al.
Chemistry
. 2023 Apr;
29(34):e202300488.
PMID: 37070368
Multiple aromatic residues assemble to form higher ordered structures known as "aromatic clusters" in proteins and play essential roles in biological systems. However, the stabilization mechanism and dynamic behavior of...
3.
Kawama K, Fukushima Y, Ikeguchi M, Ohta M, Yoshidome T
J Chem Inf Model
. 2022 Sep;
62(18):4460-4473.
PMID: 36068974
Among the factors affecting biological processes such as protein folding and ligand binding, hydration, which is represented by a three-dimensional water site distribution function around the protein, is crucial. The...
4.
Kojima R, Yoshidome T
Biophys Physicobiol
. 2021 May;
18:96-107.
PMID: 34026399
Cryo-electron microscopy (cryo-EM) is an important experimental technique for the structural analysis of biomolecules that are difficult or impossible to crystallize. The three-dimensional structure of a biomolecule can be reconstructed...
5.
Yoshidome T, Ikeguchi M, Ohta M
J Comput Chem
. 2020 Aug;
41(28):2406-2419.
PMID: 32815201
Hydration is a critical factor in the ligand binding process. Herein, to examine the hydration states of ligand binding sites, the three-dimensional distribution function for the water oxygen site, g...
6.
Oroguchi T, Yoshidome T, Yamamoto T, Nakasako M
Nano Lett
. 2018 Jul;
18(8):5192-5197.
PMID: 29990436
Cuprous oxide (CuO) particles obtained by surfactant-assisted liquid-phase synthesis have cuboid shapes but the internal structures are difficult to be visualized by electron microscopy. Herein, we investigated the internal structures...
7.
Hikiri S, Yoshidome T, Ikeguchi M
J Chem Theory Comput
. 2016 Dec;
12(12):5990-6000.
PMID: 27951672
The configurational entropy of solute molecules is a crucially important quantity to study various biophysical processes. Consequently, it is necessary to establish an efficient quantitative computational method to calculate configurational...
8.
Yoshidome T
Biophysics (Nagoya-shi)
. 2016 Nov;
7:113-122.
PMID: 27857599
We briefly review our theoretical study on the rotation scheme of F-ATPase. In the scheme, the key factor is the water entropy which has been shown to drive a variety...
9.
Yoshidome T, Oroguchi T, Nakasako M, Ikeguchi M
Phys Rev E Stat Nonlin Soft Matter Phys
. 2015 Oct;
92(3):032710.
PMID: 26465501
Coherent x-ray diffraction imaging (CXDI) enables us to visualize noncrystalline sample particles with micrometer to submicrometer dimensions. Using x-ray free-electron laser (XFEL) sources, two-dimensional diffraction patterns are collected from fresh...
10.
Yoshidome T, Ekimoto T, Matubayasi N, Harano Y, Kinoshita M, Ikeguchi M
J Chem Phys
. 2015 May;
142(17):175101.
PMID: 25956125
The hydration free energy (HFE) is a crucially important physical quantity to discuss various chemical processes in aqueous solutions. Although an explicit-solvent computation with molecular dynamics (MD) simulations is a...