Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm von Yu, Isseki, Mori, Takaharu, Ando, Tadashi, Harada, Ryuhei, Jung, Jaewoon, Sugita, Yuji, Feig, Michael

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Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics von Galvelis, Raimondas, Sugita, Yuji

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Variable Interactions between Protein Crowders and Biomolecular Solutes Are Important in Understanding Cellular Crowding von Feig, Michael, Sugita, Yuji

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Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin von Yagi, Kiyoshi, Sugita, Yuji

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Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions von Oshima, Hiraku, Sugita, Yuji

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Use of single-molecule time-series data for refining conformational dynamics in molecular simulations von Matsunaga, Yasuhiro, Sugita, Yuji

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Crowding in Cellular Environments at an Atomistic Level from Computer Simulations von Feig, Michael, Yu, Isseki, Wang, Po-hung, Nawrocki, Grzegorz, Sugita, Yuji

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GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems von Jung, Jaewoon, Tan, Cheng, Sugita, Yuji

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Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms von Mori, Takaharu, Miyashita, Naoyuki, Im, Wonpil, Feig, Michael, Sugita, Yuji

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Protein Crowding Affects Hydration Structure and Dynamics von Harada, Ryuhei, Sugita, Yuji, Feig, Michael

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The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein von Dokainish, Hisham M, Re, Suyong, Mori, Takaharu, Kobayashi, Chigusa, Jung, Jaewoon, Sugita, Yuji

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Prediction of Protein–Ligand Binding Pose and Affinity Using the gREST+FEP Method von Oshima, Hiraku, Re, Suyong, Sugita, Yuji

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Structural effects of spike protein D614G mutation in SARS-CoV-2 von Dokainish, Hisham M., Sugita, Yuji

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Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion von Matoba, Kazuaki, Kotani, Tetsuya, Tsutsumi, Akihisa, Tsuji, Takuma, Mori, Takaharu, Noshiro, Daisuke, Sugita, Yuji, Nomura, Norimichi, Iwata, So, Ohsumi, Yoshinori, Fujimoto, Toyoshi, Nakatogawa, Hitoshi, Kikkawa, Masahide, Noda, Nobuo N.

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Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments von Nawrocki, Grzegorz, Karaboga, Alp, Sugita, Yuji, Feig, Michael

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Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning von Matsunaga, Yasuhiro, Sugita, Yuji

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Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations von Tan, Cheng, Jung, Jaewoon, Kobayashi, Chigusa, Torre, Diego Ugarte La, Takada, Shoji, Sugita, Yuji

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Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations von Yagi, Kiyoshi, Yamada, Kenta, Kobayashi, Chigusa, Sugita, Yuji

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Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca2+-ATPase von Kobayashi, Chigusa, Matsunaga, Yasuhiro, Jung, Jaewoon, Sugita, Yuji

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Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape von Re, Suyong, Oshima, Hiraku, Kasahara, Kento, Kamiya, Motoshi, Sugita, Yuji

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