Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. - Shandar Ahmad; Yumlembam Hemjit Singh; Yogesh Paudel; Takaharu Mori; Yuji Sugita; Kenji Mizuguchi (BMC Bioinform., 2010)

Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation. - Suyong Re; Takashi Imai; Jaewoon Jung; Seiichiro Ten-no; Yuji Sugita (J. Comput. Chem., 2011)

Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods. - Takaharu Mori; Fumiko Ogushi; Yuji Sugita (J. Comput. Chem., 2012)

Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase. - Andrei V. Pisliakov; Tomoya Hino; Yoshitsugu Shiro; Yuji Sugita (PLoS Comput. Biol., 2012)

Efficient lookup table using a linear function of inverse distance squared. - Jaewoon Jung; Takaharu Mori; Yuji Sugita (J. Comput. Chem., 2013)

Decoupling Architecture for All-to-all Computation. - Atsushi Hori; Kazumi Yoshinaga; Atsushi Tokuhisa; Yasumasa Joti; Kensuke Okada; Takashi Sugimoto; Mitsuhiro Yamaga; Takaki Hatsui; Makina Yabashi; Yuji Sugita; Yutaka Ishikawa; Nobuhiro Go (EuroMPI/ASIA, 2014)

Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations. - Jaewoon Jung; Takaharu Mori; Yuji Sugita (J. Comput. Chem., 2014)

Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers. - Pai-Chi Li; Naoyuki Miyashita; Wonpil Im; Satoshi Ishido; Yuji Sugita (J. Comput. Chem., 2014)

Replica state exchange metadynamics for improving the convergence of free energy estimates. - Raimondas Galvelis; Yuji Sugita (J. Comput. Chem., 2015)

Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations. - Jaewoon Jung; Chigusa Kobayashi; Toshiyuki Imamura; Yuji Sugita (Comput. Phys. Commun., 2016)

Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems. - Jaewoon Jung; Yuji Sugita (J. Comput. Chem., 2017)

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms. - Chigusa Kobayashi; Jaewoon Jung; Yasuhiro Matsunaga; Takaharu Mori; Tadashi Ando; Koichi Tamura; Motoshi Kamiya; Yuji Sugita (J. Comput. Chem., 2017)

Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. - Osamu Miyashita; Chigusa Kobayashi; Takaharu Mori; Yuji Sugita; Florence Tama (J. Comput. Chem., 2017)

Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations. - Jaewoon Jung; Wataru Nishima; Marcus Daniels; Gavin Bascom; Chigusa Kobayashi; Adetokunbo Adedoyin; Michael E. Wall; Anna Lappala; Dominic Phillips; William Fischer 001; Chang-Shung Tung; Tamar Schlick; et al. (J. Comput. Chem., 2019)

De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations. - Ai Niitsu; Suyong Re; Hiraku Oshima; Motoshi Kamiya; Yuji Sugita (J. Chem. Inf. Model., 2019)

Frontiers in CryoEM Modeling. - Giulia Palermo; Yuji Sugita; Willy Wriggers; Rommie E. Amaro (J. Chem. Inf. Model., 2019)

Role of the N-Terminal Transmembrane Helix Contacts in the Activation of FGFR3. - Daisuke Matsuoka; Motoshi Kamiya; Takeshi Sato; Yuji Sugita (J. Comput. Chem., 2020)

Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method. - Hiraku Oshima; Suyong Re; Yuji Sugita (J. Chem. Inf. Model., 2020)

Faces of Contemporary CryoEM Information and Modeling. - Giulia Palermo; Yuji Sugita; Willy Wriggers; Rommie E. Amaro (J. Chem. Inf. Model., 2020)

New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems. - Jaewoon Jung; Chigusa Kobayashi; Kento Kasahara; Cheng Tan 004; Akiyoshi Kuroda; Kazuo Minami; Shigeru Ishiduki; Tatsuo Nishiki; Hikaru Inoue; Yutaka Ishikawa; Michael Feig; Yuji Sugita (J. Comput. Chem., 2021)

Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps. - Takaharu Mori; Genki Terashi; Daisuke Matsuoka; Daisuke Kihara; Yuji Sugita (J. Chem. Inf. Model., 2021)

Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins. - Ai Shinobu; Chigusa Kobayashi; Yasuhiro Matsunaga; Yuji Sugita (J. Chem. Inf. Model., 2021)

Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions. - Hiraku Oshima; Yuji Sugita (J. Chem. Inf. Model., 2022)

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. - Cheng Tan 004; Jaewoon Jung; Chigusa Kobayashi; Diego Ugarte La Torre; Shoji Takada; Yuji Sugita (PLoS Comput. Biol., 2022)

Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. - Tomonori Ogane; Daisuke Noshiro; Toshio Ando; Atsuko Yamashita; Yuji Sugita; Yasuhiro Matsunaga (PLoS Comput. Biol., 2022)

Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. - Jaewoon Jung; Chigusa Kobayashi; Yuji Sugita (J. Comput. Chem., 2023)

Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study. - Azuki Mizutani; Cheng Tan 004; Yuji Sugita; Shoji Takada (PLoS Comput. Biol., 2023)

SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations. - Isseki Yu; Takaharu Mori; Daisuke Matsuoka; Donatas Surblys; Yuji Sugita (J. Comput. Chem., 2024)

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. - Diego Ugarte La Torre; Jaewoon Jung; Yuji Sugita (HPC Asia, 2025)