| 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 | 283 | 2016 |
| 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 | 180 | 2015 |
| 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 | 157 | 2017 |
| 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 | 119 | 2019 |
| 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 | 54 | 2013 |
| 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, 1-12, 2021 | 53 | 2021 |
| 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 | 47 | 2021 |
| 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 | 42 | 2022 |
| Assessment of free energy expressions in RISM integral equation theory: theoretical prediction of partition coefficients revisited S Ten-no, J Jung, H Chuman, Y Kawashima Molecular Physics 108 (3-4), 327-332, 2010 | 42 | 2010 |
| Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations C Tan, J Jung, C Kobayashi, DUL Torre, S Takada, Y Sugita PLOS Computational Biology 18 (4), e1009578, 2022 | 38 | 2022 |
| Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations J Jung, C Kobayashi, T Imamura, Y Sugita Computer Physics Communications 200, 57-65, 2016 | 36 | 2016 |
| 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 | 32 | 2016 |
| 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 | 28 | 2014 |
| New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals J Jung, CH Choi, Y Sugita, S Ten-No The Journal of Chemical Physics 127 (20), 2007 | 28 | 2007 |
| 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 | 26 | 2013 |
| Graphics processing unit acceleration and parallelization of GENESIS for large-scale molecular dynamics simulations J Jung, A Naurse, C Kobayashi, Y Sugita Journal of Chemical Theory and Computation 12 (10), 4947-4958, 2016 | 25 | 2016 |
| Topological determinants of protein unfolding rates J Jung, J Lee, HT Moon PROTEINS: Structure, Function, and Bioinformatics 58 (2), 389-395, 2005 | 25 | 2005 |
| 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 | 21 | 2021 |
| 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 (1), 161-174. e3, 2019 | 20 | 2019 |
| Optimal temperature evaluation in molecular dynamics simulations with a large time step J Jung, C Kobayashi, Y Sugita Journal of chemical theory and computation 15 (1), 84-94, 2019 | 18 | 2019 |
Yuji SugitaRIKENVerified email at riken.go.jp
