Yuji Sugita

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 20

Top Topics

Biological Systems

Parallel Computing

Molecular Dynamics

Protein Folding

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

PLoS Comput. Biol.

Comput. Phys. Commun.

Publications

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) (2024)
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)
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) (2023)
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)
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) (2022)
Hiraku Oshima, Yuji Sugita
Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions. J. Chem. Inf. Model. 62 (11) (2022)
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) (2021)
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) (2021)
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) (2021)
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) (2020)
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) (2020)
Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro
Faces of Contemporary CryoEM Information and Modeling. J. Chem. Inf. Model. 60 (5) (2020)
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) (2019)
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) (2019)
Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro
Frontiers in CryoEM Modeling. J. Chem. Inf. Model. 59 (7) (2019)
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) (2017)
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) (2017)
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) (2017)
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 (2016)
Raimondas Galvelis, Yuji Sugita
Replica state exchange metadynamics for improving the convergence of free energy estimates. J. Comput. Chem. 36 (19) (2015)
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)
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) (2014)
Jaewoon Jung, Takaharu Mori, Yuji Sugita
Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations. J. Comput. Chem. 35 (14) (2014)
Jaewoon Jung, Takaharu Mori, Yuji Sugita
Efficient lookup table using a linear function of inverse distance squared. J. Comput. Chem. 34 (28) (2013)
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) (2012)
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)
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) (2011)
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 (2010)