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Takaharu Mori
Takaharu Mori
Verified email at rs.tus.ac.jp
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Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion
K Matoba, T Kotani, A Tsutsumi, T Tsuji, T Mori, D Noshiro, Y Sugita, ...
Nature structural & molecular biology 27 (12), 1185-1193, 2020
3012020
Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
I Yu, T Mori, T Ando, R Harada, J Jung, Y Sugita, M Feig
Elife 5, e19274, 2016
2922016
Conformational transition of Sec machinery inferred from bacterial SecYE structures
T Tsukazaki, H Mori, S Fukai, R Ishitani, T Mori, N Dohmae, A Perederina, ...
Nature 455 (7215), 988-991, 2008
2822008
Structural basis of Sec-independent membrane protein insertion by YidC
K Kumazaki, S Chiba, M Takemoto, A Furukawa, K Nishiyama, Y Sugano, ...
Nature 509 (7501), 516-520, 2014
2522014
GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
J Jung, T Mori, C Kobayashi, Y Matsunaga, T Yoda, M Feig, Y Sugita
Wiley Interdisciplinary Reviews: Computational Molecular Science 5 (4), 310-323, 2015
1842015
GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
C Kobayashi, J Jung, Y Matsunaga, T Mori, T Ando, K Tamura, M Kamiya, ...
Journal of Computational Chemistry 38 (25), 2193-2206, 2017
1592017
Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms
T Mori, N Miyashita, W Im, M Feig, Y Sugita
Biochimica et Biophysica Acta (BBA)-Biomembranes 1858 (7), 1635-1651, 2016
1452016
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology
M Feig, R Harada, T Mori, I Yu, K Takahashi, Y Sugita
Journal of Molecular Graphics and Modelling 58, 1-9, 2015
862015
Crystal structures of SecYEG in lipidic cubic phase elucidate a precise resting and a peptide-bound state
Y Tanaka, Y Sugano, M Takemoto, T Mori, A Furukawa, T Kusakizako, ...
Cell reports 13 (8), 1561-1568, 2015
782015
Surface-tension replica-exchange molecular dynamics method for enhanced sampling of biological membrane systems
T Mori, J Jung, Y Sugita
Journal of Chemical Theory and Computation 9 (12), 5629-5640, 2013
552013
Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein
T Mori, J Jung, C Kobayashi, HM Dokainish, S Re, Y Sugita
Biophysical journal 120 (6), 1060-1071, 2021
532021
Flexible fitting to cryo‐EM density map using ensemble molecular dynamics simulations
O Miyashita, C Kobayashi, T Mori, Y Sugita, F Tama
Journal of computational chemistry 38 (16), 1447-1461, 2017
532017
The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein
HM Dokainish, S Re, T Mori, C Kobayashi, J Jung, Y Sugita
Elife 11, e75720, 2022
462022
Tunnel formation inferred from the I-form structures of the proton-driven protein secretion motor SecDF
A Furukawa, K Yoshikaie, T Mori, H Mori, YV Morimoto, Y Sugano, S Iwaki, ...
Cell Reports 19 (5), 895-901, 2017
452017
Dynamics of nitric oxide controlled by protein complex in bacterial system
E Terasaka, K Yamada, PH Wang, K Hosokawa, R Yamagiwa, ...
Proceedings of the National Academy of Sciences 114 (37), 9888-9893, 2017
422017
Analysis of lipid surface area in protein–membrane systems combining voronoi tessellation and monte carlo integration methods
T Mori, F Ogushi, Y Sugita
Journal of computational chemistry 33 (3), 286-293, 2012
402012
Dimensionality of collective variables for describing conformational changes of a multi-domain protein
Y Matsunaga, Y Komuro, C Kobayashi, J Jung, T Mori, Y Sugita
The Journal of Physical Chemistry Letters 7 (8), 1446-1451, 2016
342016
Midpoint cell method for hybrid (MPI+ OpenMP) parallelization of molecular dynamics simulations
J Jung, T Mori, Y Sugita
Journal of computational chemistry 35 (14), 1064-1072, 2014
292014
Efficient lookup table using a linear function of inverse distance squared
J Jung, T Mori, Y Sugita
Journal of Computational Chemistry 34 (28), 2412-2420, 2013
262013
Optimized hydrogen mass repartitioning scheme combined with accurate temperature/pressure evaluations for thermodynamic and kinetic properties of biological systems
J Jung, K Kasahara, C Kobayashi, H Oshima, T Mori, Y Sugita
Journal of Chemical Theory and Computation 17 (8), 5312-5321, 2021
252021
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