Yuji Sugita

32 papers C 1Journal 30Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
An Empirical Biasing Force Constant to Minimize Overfitting in Cryo-EM Flexible Fitting Refinement.
J. Chem. Inf. Model.
Daisuke Matsuoka, Yuji Sugita, Takaharu Mori
2025 J jnl
CGBack: Diffusion Model for Backmapping Large-Scale and Complex Coarse-Grained Molecular Systems.
J. Chem. Inf. Model.
Diego Ugarte La Torre, Yuji Sugita
2025 J jnl
ColBuilder: flexible structure generation of crosslinked collagen fibrils.
Bioinform.
Debora Monego, Matthias Brosz, Johanna Buck, Vsevolod Viliuga, Paulius Greicius, Jaewoon Jung, Torsten Stuehn, Matthias Schmies, Yuji Sugita, Frauke Gräter
2025 C conf
Scaling molecular dynamics for large-scale simulation of biological systems on AMD CPU/GPU supercomputers: Lessons from LUMI: Optimizing GENESIS for maximizing the computational efficiency of CPU and GPU kernels on the LUMI supercomputer.
HPC Asia
Diego Ugarte La Torre, Jaewoon Jung, Yuji Sugita
2024 J jnl
SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations.
J. Comput. Chem.
Isseki Yu, Takaharu Mori, Daisuke Matsuoka, Donatas Surblys, Yuji Sugita
2023 J jnl
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer.
J. Comput. Chem.
Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
2023 J jnl
Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study.
PLoS Comput. Biol.
Azuki Mizutani, Cheng Tan, Yuji Sugita, Shoji Takada
2022 J jnl
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images.
PLoS Comput. Biol.
Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga
2022 J jnl
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.
PLoS Comput. Biol.
Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, Yuji Sugita
2022 J jnl
Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions.
J. Chem. Inf. Model.
Hiraku Oshima, Yuji Sugita
2021 J jnl
Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins.
J. Chem. Inf. Model.
Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, Yuji Sugita
2021 J jnl
Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.
J. Chem. Inf. Model.
Takaharu Mori, Genki Terashi, Daisuke Matsuoka, Daisuke Kihara, Yuji Sugita
2021 J jnl
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems.
J. Comput. Chem.
Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, Yuji Sugita
2020 J jnl
Faces of Contemporary CryoEM Information and Modeling.
J. Chem. Inf. Model.
Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro
2020 J jnl
Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method.
J. Chem. Inf. Model.
Hiraku Oshima, Suyong Re, Yuji Sugita
2020 J jnl
Role of the N-Terminal Transmembrane Helix Contacts in the Activation of FGFR3.
J. Comput. Chem.
Daisuke Matsuoka, Motoshi Kamiya, Takeshi Sato, Yuji Sugita
2019 J jnl
De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations.
J. Chem. Inf. Model.
Ai Niitsu, Suyong Re, Hiraku Oshima, Motoshi Kamiya, Yuji Sugita
2019 J jnl
Frontiers in CryoEM Modeling.
J. Chem. Inf. Model.
Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro
2019 J jnl
Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations.
J. Comput. Chem.
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
2017 J jnl
Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations.
J. Comput. Chem.
Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, Florence Tama
2017 J jnl
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.
J. Comput. Chem.
Chigusa Kobayashi, Jaewoon Jung, Yasuhiro Matsunaga, Takaharu Mori, Tadashi Ando, Koichi Tamura, Motoshi Kamiya, Yuji Sugita
2017 J jnl
Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems.
J. Comput. Chem.
Jaewoon Jung, Yuji Sugita
2016 J jnl
Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations.
Comput. Phys. Commun.
Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, Yuji Sugita
2015 J jnl
Replica state exchange metadynamics for improving the convergence of free energy estimates.
J. Comput. Chem.
Raimondas Galvelis, Yuji Sugita
2014 — conf
Decoupling Architecture for All-to-all Computation.
EuroMPI/ASIA
Atsushi Hori, Kazumi Yoshinaga, Atsushi Tokuhisa, Yasumasa Joti, Kensuke Okada, Takashi Sugimoto, Mitsuhiro Yamaga, Takaki Hatsui, Makina Yabashi, Yuji Sugita, Yutaka Ishikawa, Nobuhiro Go
2014 J jnl
Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations.
J. Comput. Chem.
Jaewoon Jung, Takaharu Mori, Yuji Sugita
2014 J jnl
Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers.
J. Comput. Chem.
Pai-Chi Li, Naoyuki Miyashita, Wonpil Im, Satoshi Ishido, Yuji Sugita
2013 J jnl
Efficient lookup table using a linear function of inverse distance squared.
J. Comput. Chem.
Jaewoon Jung, Takaharu Mori, Yuji Sugita
2012 J jnl
Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods.
J. Comput. Chem.
Takaharu Mori, Fumiko Ogushi, Yuji Sugita
2012 J jnl
Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase.
PLoS Comput. Biol.
Andrei V. Pisliakov, Tomoya Hino, Yoshitsugu Shiro, Yuji Sugita
2011 J jnl
Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation.
J. Comput. Chem.
Suyong Re, Takashi Imai, Jaewoon Jung, Seiichiro Ten-no, Yuji Sugita
2010 J jnl
Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins.
BMC Bioinform.
Shandar Ahmad, Yumlembam Hemjit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi