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Journal Articles
- 2024
[j27]Isseki Yu, Takaharu Mori, Daisuke Matsuoka, Donatas Surblys, Yuji Sugita
:
SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations. J. Comput. Chem. 45(8): 498-505 (2024)- 2023
- [j26]Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita:
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. J. Comput. Chem. 44(20): 1740-1749 (2023) - [j25]Azuki Mizutani, Cheng Tan, Yuji Sugita, Shoji Takada:
Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study. PLoS Comput. Biol. 19(7) (2023) - 2022
- [j24]Hiraku Oshima, Yuji Sugita:
Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions. J. Chem. Inf. Model. 62(11): 2846-2856 (2022) - [j23]Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, Yuji Sugita:
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. PLoS Comput. Biol. 18(4) (2022) - [j22]Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga:
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. PLoS Comput. Biol. 18(12): 1010384 (2022) - 2021
- [j21]Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, Yuji Sugita:
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems. J. Comput. Chem. 42(4): 231-241 (2021) - [j20]Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, Yuji Sugita:
Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins. J. Chem. Inf. Model. 61(5): 2427-2443 (2021) - [j19]Takaharu Mori, Genki Terashi, Daisuke Matsuoka, Daisuke Kihara, Yuji Sugita:
Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps. J. Chem. Inf. Model. 61(7): 3516-3528 (2021) - 2020
- [j18]Daisuke Matsuoka, Motoshi Kamiya, Takeshi Sato, Yuji Sugita:
Role of the N-Terminal Transmembrane Helix Contacts in the Activation of FGFR3. J. Comput. Chem. 41(6): 561-572 (2020) - [j17]Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro:
Faces of Contemporary CryoEM Information and Modeling. J. Chem. Inf. Model. 60(5): 2407-2409 (2020) - [j16]Hiraku Oshima, Suyong Re, Yuji Sugita:
Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method. J. Chem. Inf. Model. 60(11): 5382-5394 (2020) - 2019
- [j15]Jaewoon Jung, Wataru Nishima, Marcus Daniels, Gavin Bascom, Chigusa Kobayashi, Adetokunbo Adedoyin, Michael E. Wall, Anna Lappala, Dominic Phillips, William Fischer, Chang-Shung Tung, Tamar Schlick, Yuji Sugita, Karissa Y. Sanbonmatsu:
Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations. J. Comput. Chem. 40(21): 1919-1930 (2019) - [j14]Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro:
Frontiers in CryoEM Modeling. J. Chem. Inf. Model. 59(7): 3091-3093 (2019) - [j13]Ai Niitsu, Suyong Re, Hiraku Oshima, Motoshi Kamiya, Yuji Sugita:
De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations. J. Chem. Inf. Model. 59(9): 3879-3888 (2019) - 2017
- [j12]Jaewoon Jung, Yuji Sugita:
Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems. J. Comput. Chem. 38(16): 1410-1418 (2017) - [j11]Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, Florence Tama:
Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. J. Comput. Chem. 38(16): 1447-1461 (2017) - [j10]Chigusa Kobayashi, Jaewoon Jung, Yasuhiro Matsunaga, Takaharu Mori, Tadashi Ando, Koichi Tamura, Motoshi Kamiya, Yuji Sugita:
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms. J. Comput. Chem. 38(25): 2193-2206 (2017) - 2016
- [j9]Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, Yuji Sugita:
Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations. Comput. Phys. Commun. 200: 57-65 (2016) - 2015
- [j8]Raimondas Galvelis, Yuji Sugita:
Replica state exchange metadynamics for improving the convergence of free energy estimates. J. Comput. Chem. 36(19): 1446-1455 (2015) - 2014
- [j7]Pai-Chi Li, Naoyuki Miyashita, Wonpil Im, Satoshi Ishido, Yuji Sugita:
Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers. J. Comput. Chem. 35(4): 300-308 (2014) - [j6]Jaewoon Jung, Takaharu Mori, Yuji Sugita:
Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations. J. Comput. Chem. 35(14): 1064-1072 (2014) - 2013
- [j5]Jaewoon Jung, Takaharu Mori, Yuji Sugita:
Efficient lookup table using a linear function of inverse distance squared. J. Comput. Chem. 34(28): 2412-2420 (2013) - 2012
- [j4]Takaharu Mori, Fumiko Ogushi, Yuji Sugita:
Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods. J. Comput. Chem. 33(3): 286-293 (2012) - [j3]Andrei V. Pisliakov, Tomoya Hino, Yoshitsugu Shiro, Yuji Sugita:
Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase. PLoS Comput. Biol. 8(8) (2012) - 2011
- [j2]Suyong Re, Takashi Imai, Jaewoon Jung, Seiichiro Ten-no, Yuji Sugita:
Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation. J. Comput. Chem. 32(2): 260-270 (2011) - 2010
- [j1]Shandar Ahmad, Yumlembam Hemjit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi:
Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. BMC Bioinform. 11: 533 (2010)
Conference and Workshop Papers
- 2014
- [c1]Atsushi Hori, Kazumi Yoshinaga, Atsushi Tokuhisa, Yasumasa Joti, Kensuke Okada, Takashi Sugimoto, Mitsuhiro Yamaga, Takaki Hatsui, Makina Yabashi, Yuji Sugita, Yutaka Ishikawa, Nobuhiro Go:
Decoupling Architecture for All-to-all Computation. EuroMPI/ASIA 2014: 169
Coauthor Index
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