Články s príkazom na verejný prístup - Yuji SugitaĎalšie informácie
Nedostupné nikde: 3
Water orientation at ceramide/water interfaces studied by heterodyne-detected vibrational sum frequency generation spectroscopy and molecular dynamics simulation
A Adhikari, S Re, W Nishima, M Ahmed, S Nihonyanagi, JB Klauda, ...
The Journal of Physical Chemistry C 120 (41), 23692-23697, 2016
Príkazy: US National Science Foundation
SPANA: Spatial decomposition analysis for cellular‐scale molecular dynamics simulations
I Yu, T Mori, D Matsuoka, D Surblys, Y Sugita
Journal of Computational Chemistry 45 (8), 498-505, 2024
Príkazy: Japan Science and Technology Agency
Deciphering the multi-state conformational equilibrium of HDM2 in the regulation of p53 binding: Perspectives from molecular dynamics simulation and NMR analysis
K Watanabe, Q Zhao, R Iwatsuki, R Fukui, W Ren, Y Sugita, N Nishida
Journal of the American Chemical Society 146 (14), 9790-9800, 2024
Príkazy: Japan Science and Technology Agency
Dostupné niekde: 44
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
Príkazy: US National Science Foundation, US National Institutes of Health
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
Príkazy: US National Institutes of Health
Protein crowding affects hydration structure and dynamics
R Harada, Y Sugita, M Feig
Journal of the American Chemical Society 134 (10), 4842-4849, 2012
Príkazy: US National Institutes of Health
Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT
S Doki, HE Kato, N Solcan, M Iwaki, M Koyama, M Hattori, N Iwase, ...
Proceedings of the National Academy of Sciences 110 (28), 11343-11348, 2013
Príkazy: UK Medical Research Council, Wellcome Trust
Crowding in cellular environments at an atomistic level from computer simulations
M Feig, I Yu, P Wang, G Nawrocki, Y Sugita
The Journal of Physical Chemistry B 121 (34), 8009-8025, 2017
Príkazy: US National Science Foundation, US National Institutes of Health
Reduced native state stability in crowded cellular environment due to protein–protein interactions
R Harada, N Tochio, T Kigawa, Y Sugita, M Feig
Journal of the American Chemical Society 135 (9), 3696-3701, 2013
Príkazy: US National Institutes of Health
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
Príkazy: US National Science Foundation, US National Institutes of Health
Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding
M Feig, Y Sugita
The Journal of Physical Chemistry B 116 (1), 599-605, 2012
Príkazy: US National Institutes of Health
Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations
J Jung, W Nishima, M Daniels, G Bascom, C Kobayashi, A Adedoyin, ...
Journal of computational chemistry 40 (21), 1919-1930, 2019
Príkazy: US Department of Energy, US National Institutes of Health
Slow-down in diffusion in crowded protein solutions correlates with transient cluster formation
G Nawrocki, P Wang, I Yu, Y Sugita, M Feig
The Journal of Physical Chemistry B 121 (49), 11072-11084, 2017
Príkazy: US National Science Foundation, US National Institutes of Health
Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations
N Miyashita, JE Straub, D Thirumalai, Y Sugita
Journal of the American Chemical Society 131 (10), 3438-3439, 2009
Príkazy: US National Institutes of Health
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
Príkazy: US National Institutes of Health
CHARMM-GUI free energy calculator for absolute and relative ligand solvation and binding free energy simulations
S Kim, H Oshima, H Zhang, NR Kern, S Re, J Lee, B Roux, Y Sugita, ...
Journal of chemical theory and computation 16 (11), 7207-7218, 2020
Príkazy: US National Science Foundation, US Department of Energy, US National …
Dynamics and interactions of OmpF and LPS: influence on pore accessibility and ion permeability
DS Patel, S Re, EL Wu, Y Qi, PE Klebba, G Widmalm, MS Yeom, Y Sugita, ...
Biophysical journal 110 (4), 930-938, 2016
Príkazy: US National Science Foundation, US National Institutes of Health, Swedish …
Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study
R Ishitani, Y Sugita, N Dohmae, N Furuya, M Hattori, O Nureki
Proceedings of the National Academy of Sciences 105 (40), 15393-15398, 2008
Príkazy: US National Institutes of Health
Reaching new levels of realism in modeling biological macromolecules in cellular environments
M Feig, Y Sugita
Journal of Molecular Graphics and Modelling 45, 144-156, 2013
Príkazy: US National Institutes of Health
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems
J Jung, C Kobayashi, K Kasahara, C Tan, A Kuroda, K Minami, S Ishiduki, ...
Journal of computational chemistry 42 (4), 231-241, 2021
Príkazy: US National Institutes of Health
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