- Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning.
T. Mori, M. Kulik, O. Miyashita, J. Jung, F. Tama, Y. Sugita
Structure, 27, 161-174 (2019).
- Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides.
M. Kulik, T. Mori, Y. Sugita, J. Trylska
Nucleic Acids Research, 46, 9960-9970 (2018).
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Dynamics of nitric oxide controlled by protein complex in bacterial system.
E. Terasaka, K. Yamada, P.-H. Wang, K. Hosokawa, R. Yamagiwa, K. Matsumoto, S. Ishii, T. Mori, K. Yagi, H. Sawai, H. Arai, H. Sugimoto, Y. Sugita, Y. Shiro, and T. Tosha.
Proc. Natl. Acad. Sci., U.S.A., 114, 9888-9893 (2017).
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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, and Y. Sugita.
J. Comput. Chem., 38, 2193-2206 (2017).
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Discrimination of native-like states of membrane proteins with implicit membrane-based scoring functions.
B. Dutagaci, K. Wittayanarakul, T. Mori, M. Feig.
J. Chem. Theory Comput., 13, 3049-3059 (2017).
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Tunnel formation inferred from the I-form structures of the proton-driven protein secretion motor SecDF.
A. Furukawa, K. Yoshikaie, T. Mori, H. Mori, Y. V. Morimoto, Y. Sugano, S. Iwaki, T. Minamino, Y. Sugita, Y. Tanaka, and T. Tsukazaki.
Cell Rep., 19, 895-901 (2017).
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Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations.
O. Miyashita, C. Kobayashi, T. Mori, Y. Sugita, and F. Tama.
J. Comput. Chem., 38, 1447-1461 (2017).
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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, and M. Feig.
eLife, 5, e19274 (2016).
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Dimensionality of collective variables for describing conformational changes of a multi-domain protein.
Y. Matsunaga, Y. Komuro, C. Kobayashi, J. Jung, T. Mori, and Y. Sugita.
J. Phys. Chem. Lett., 7, 1446-1451 (2016).
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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, K. Kumazaki, A. Kashima, R. Ishitani, Y. Sugita, O. Nureki, and T. Tsukazaki.
Cell Reports, 13, 1561-1568 (2015).
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Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.
M. Feig, R. Harada, T. Mori, I. Yu, K. Takahashi and Y. Sugita.
J. Mol. Graph. Model., 58, 1-9 (2015).
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Structural basis of Sec-independent membrane protein insertion by YidC.
K. Kumazaki, S. Chiba, M. Takemoto, A. Furukawa, K. Nishiyama, Y. Sugano, T. Mori, N. Dohmae, K. Hirata, Y. Nakada-Nakura, A. D. Maturana, Y. Tanaka, H. Mori, Y. Sugita, F. Arisaka, K. Ito, R. Ishitani, T. Tsukazaki, and O. Nureki.
Nature, 509, 516-520 (2014).
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Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations.
J. Jung, T. Mori, and Y. Sugita.
J. Comput. Chem., 35, 1064-1072 (2014).
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Surface-tension replica-exchange moleclar dynamics method for enhanced sampling of biological membrane systems.
T. Mori, J. Jung, and Y. Sugita.
J. Chem. Theory Comput., 9, 5629-5640 (2013).
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Efficient lookup table using a linear function of inverse distance squared.
J. Jung, T. Mori, and Y. Sugita.
J. Comput. Chem., 34, 2412-2420 (2013).
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Energetics of the presequence-binding poses in mitochondrial protein import through Tom20.
Y. Komuro, N. Miyashita, T. Mori, E. Muneyuki, T. Saitoh, D. Kohda, and Y. Sugita.
J. Phys. Chem. B, 117, 2864–2871 (2013).
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Analysis of lipid surface area in protein-membrane systems combining Voronoi tessellation and Monte Carlo integration methods.
T. Mori, F. Ogushi, and Y. Sugita.
J. Comput. Chem., 33, 286-293 (2012).
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Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data.
M. Morita, A. V. S. K. Krishna Mohan, S. Ahmad, T. Mori, Y. Sugita, and K. Mizuguchi.
BMC Biophysics, 4, 21 (2011).
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Dynamic structure of the polytheonamide B channel studied by normal mode analysis.
T. Mori, H. Kokubo, S. Oiki, and Y. Okamoto.
Mol. Simul., 37, 975-985 (2011).
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Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins.
S. Ahmad, Y. H. Singh, Y. Paudel, T. Mori, Y. Sugita, and K. Mizuguchi.
BMC Bioinformatics, 11, 533 (2010).
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Molecular mechanisms underlying the early stage of protein translocation through the Sec translocon.
T. Mori, R. Ishitani, T. Tsukazaki, O. Nureki, and Y. Sugita.
Biochemistry, 49, 945-950 (2010).
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Folding simulations of gramicidin A into the β-helix conformations: Simulated annealing molecular dynamics study.
T. Mori and Y. Okamoto.
J. Chem. Phys., 131, 165103 (2009).
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Conformational transition of Sec machinery inferred from bacterial SecYE structures.
T. Tsukazaki, H. Mori, S. Fukai, R. Ishitani, T. Mori, N. Dohmae, A. Perederina, Y. Sugita, D. G. Vassylyev, K. Ito, and O. Nureki.
Nature, 455, 988-992 (2008).
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Estimation of dye configuration from conventional chiroptical spectra of porphyrin Integrates: Combination of exciton theory with Monte Carlo molecular structural simulation.
T. Yamamura, T. Mori, Y. Tsuda, T. Taguchi, and N. Josha.
J. Phys. Chem. A, 111, 2128-2138 (2007).
