GENESIS Related Publications

2025

• Langevin integration for isothermal–isobaric condition with a large time step
  Jaewoon Jung, Yuji Sugita
  J. Chem. Phys. 162, 10, 104108, (2025).

• Scaling molecular dynamics for large-scale simulation of biological systems on AMD CPU/GPU supercomputers: Lessons from LUMI
  Diego Ugarte La Torre, Jaewoon Jung, Yuji Sugita
  Proc. Int. Conf. High Perform. Comput. Asia-Pacific Region (HPCAsia ’25), 1–12, (2025).

2024

• Fusion Dynamics and Size-Dependence of Droplet Microstructure in ssDNA-Mediated Protein Phase Separation
  Yunqiang Bian, Fangyi Lv, Hai Pan, Weitong Ren, Weiwei Zhang, Yanwei Wang, Yi Cao, Wenfei Li, Wei Wang
  JACS Au 4, 3690−3704, (2024).

• Predicting Heteropolymer Interactions: Demixing and Hypermixing of Disordered Protein Sequences
  Kyosuke Adachi, Kyogo Kawaguchi
  Phys. Rev. X 14, 031011, (2024).

• GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models
  Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
  J. Phys. Chem. B 128, 25, 6028–6048, (2024).

• Learning QM/MM potential using equivariant multiscale model
  Yao-Kun Lei, Kiyoshi Yagi, Yuji Sugita
  J. Chem. Phys. 160, 214109, (2024).

• Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State Model
  Masao Inoue, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi
  J. Chem. Inf. Model. 64, 3884−3895, (2024).

• GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems
  Jaewoon Jung, Cheng Tan, Yuji Sugita
  Nature Communications 15, 3370, (2024).

• Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch
  Piotr Chyzy, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska
  Proc. Natl. Acad. Sci. USA 121, 15, e2317197121, (2024).

• Free-energy landscapes of transmembrane homodimers by bias-exchange adaptively biased molecular dynamics
  Shingo Ito, Yuji Sugita
  Biophys. Chem. 307, 107190, (2024).

2023

• SPANA: Spatial Decomposition Analysis for Cellular-Scale Molecular Dynamics Simulations
  Isseki Yu, Takaharu Mori, Daisuke Matsuoka, Donatas Surblys, Yuji Sugita
  J. Comput. Chem. 45, 498-505, (2023).

• Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers
  Diego Ugarte, Shoji Takada, Yuji Sugita
  J. Chem. Phys. 159, 075101, (2023).

• Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study
  Azuki Mizutani, Cheng Tan, Yuji Sugita, Shoji Takada
  PLOS Computational Biology 19, e1011321, (2023).

• Structural Effects of Spike Protein D614G Mutation in SARS-CoV-2
  Hisham Dokainish, Yuji Sugita
  Biophys. J. 122, 2910-2920, (2023).

• 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. 44, 1740-1749, (2023).

• Highly charged proteins and their repulsive interactions antagonize biomolecular condensation
  Cheng Tan, Ai Niitsu, Yuji Sugita
  JACS Au 3, 834-848, (2023).

• Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding
  Shingo Ito, Kyoshi Yagi, Yuji Sugita
  J. Chem. Phys. 158, 115101, (2023).

• Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation
  Ai Niitsu, Yuji Sugita
  Phys. Chem. Chem. Phys. 25, 3595-3606, (2023).

2022

• Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation
  Yasuhiro Matsunaga, Motoshi Kamiya, Hiraku Oshima, Jaewoon Jung, Shingo Ito, Yuji Sugita
  Biophys. Rev. 14, 1503–1512, (2022).

• Modified protein-water interactions in CHARMM36m for thermodynamics and kinetics of proteins in dilute and crowded solutions
  Daiki Matsubara, Kento Kasahara, Hisham Dokainish, Hiraku Oshima, Yuji Sugita
  Molecules 27, 5726, (2022).

• Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions
  Hiraku Oshima, Yuji Sugita
  Journal of Chemical Information and Modeling 62, 2846–2856,(2022).

• Computational Analysis on the Allostery of Tryptophan Synthase: Relationship between α/β-Ligand Binding and Distal Domain Closure
  Shingo Ito, Kiyoshi Yagi, Yuji Sugita
  The Journal of Physical Chemistry B 126, 17, 3300-3308, (2022).

• Protein Folding Intermediates on the Dimensionality Reduced Landscape with UMAP and Native Contact Likelihood
  Mao Oide, Yuji Sugita
  J. Chem. Phys. 157, 075101, (2022).

• Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics
  Ai Shinobu, Suyong Re, Yuji Sugita
  Frontiers in Molecular Biosciences 9, 878830, (2022).

• Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
  Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, Yuji Sugita
  PLOS Computational Biology 18, e1009578, (2022).

• The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein
  Hisham M Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung, Yuji Sugita
  eLife 11, e75720, (2022).

2021

• Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca2+-ATPase
  Chigusa Kobayashi, Yasuhiro Matsunaga, Jaewoon Jung, Yuji Sugita
  Proc. Natl. Acad. Sci. USA 118, e2105507118, (2021).

• Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations
  Weitong Ren, Hisham M. Dokainish, Ai Shinobu, Hiraku Oshima, Yuji Sugita
  The Journal of Physical Chemistry B 125, 2898–2909, (2021).

• Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin
  Kiyoshi Yagi, Yuji Sugita
  J. Chem. Theory Comput. 17, 5007–5020, (2021).

• Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems
  Jaewoon Jung, Kento Kasahara, Chigusa Kobayashi, Hiraku Oshima, Takaharu Mori, Yuji Sugita
  J. Chem. Theory Comput. 17, 5312–5321, (2021).

• Reduced efficacy of a Src kinase inhibitor in crowded protein solution
  Kento Kasahara, Suyong Re, Grzegorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Miyata-Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael Feig, Yuji Sugita
  Nature Communications 12, 4099, (2021).

• Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations
  Toru Ekimoto, Takafumi Kudo, Tsutomu Yamane, Mitsunori Ikeguchi
  J. Chem. Inf. Model. 61, 3625−3637, (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. 61, 3516–3528, (2021).

• Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection
  Piotr Chyzy, Marta Kulik, Suyong Re, Yuji Sugita, Joanna Trylska
  Frontiers in Molecular Biosciences 8, 633130, (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. 61, 2427–2443, (2021).

• Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations
  Kiyoshi Yagi, Shingo Ito, Yuji Sugita
  J. Phys. Chem. B 125, 4701–4713, (2021).

• Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein
  Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita
  Biophys. J. 120, 1060–1071, (2021).

• Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution
  Marta Kulik, Takaharu Mori, Yuji Sugita
  Front. Mol. Biosci. 8, 631854, (2021).

• New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems
  Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, Yuji Sugita
  J. Comput. Chem. 42, 231–241, (2021).

2020

• Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling
  Hisham M. Dokainish, Yuji Sugita
  International Journal of Molecular Sciences 22, 270, (2020).

• Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step
  Jaewoon Jung, Yuji Sugita
  J. Chem. Phys. 153, 234115, (2020).

• Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method
  Hiraku Oshima, Suyong Re, Yuji Sugita
  J. Chem. Inf. Model. 60, 5382–5394, (2020).

• A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations
  Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
  J. Chem. Phys. 153, 044110, (2020).

• Implicit Micelle Model for Membrane Proteins Using Superellipsoid Approximation
  Takaharu Mori, Yuji Sugita
  J. Chem. Theory Comput. 16, 711–724, (2020).

• Role of the N-Terminal Transmembrane Helix Contacts in the Activation of FGFR3
  Daisuke Matsuoka, Motoshi Kamiya, Takeshi Sato, Yuji Sugita
  J. Comput. Chem. 41, 561–572, (2020).

2019

• Building a macro-mixing dual‑basin Go model using the Multistate Bennett Acceptance Ratio
  Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, Yuji Sugita
  Biophysics and Physicobiology 16, 310–321, (2019).

• Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape
  Suyong Re, Hiraku Oshima, Kento Kasahara, Motoshi Kamiya, Yuji Sugita
  Proc. Natl. Acad. Sci. USA 116, 18404–18409, (2019).

• Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules
  Hiraku Oshima, Suyong Re, Yuji Sugita
  J. Chem. Theory Comput. 15, 5199–5208, (2019).

• 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 Wall, Anna Lappala, Dominic Phillips, William Fischer, Chang-Shung Tung, Tamar Schlick, Yuji Sugita, Karissa Y. Sanbonmatsu
  J. Comput. Chem. 40, 1919–1930, (2019).

• Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations
  Kiyoshi Yagi, Kenta Yamada, Chigusa Kobayashi, Yuji Sugita
  Journal of Chemical Theory and Computation 15, 1924–1938,(2019).

• Population Shift Mechanism for Partial Agonism of AMPA Receptor
  Hiraku Oshima, Suyong Re, Masayoshi Sakakura, Hideo Takahashi, Yuji Sugita
  Biophysical Journal 116, 57–68, (2019).

• Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning
  Takaharu Mori, Marta Kulik, Osamu Miyashita, Jaewoon Jung, Florence Tama, Yuji Sugita
  Structure 27, 161–174, (2019).

• Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step
  Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
  Journal of Chemical Theory and Computation 15, 84–94, (2019).

2018

• Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides
  Marta Kulik, Takaharu Mori, Yuji Sugita, Joanna Trylska
  Nucleic Acids Research 46, 19, 9960–9970, (2018).

• Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning
  Yasuhiro Matsunaga, Yuji Sugita
  eLife 7, e32668, (2018).

• Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories
  Y. Matsunaga, Y. Sugita
  The Journal of Chemical Physics 148, 241731, (2018).

• Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation
  Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
  The Journal of Chemical Physics 148, 164109, (2018).

• Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations
  Motoshi Kamiya, Yuji Sugita
  The Journal of Chemical Physics 149, 072304, (2018).

2017

• Dynamics of nitric oxide controlled by protein complex in bacterial system
  Erina Terasaka, Kenta Yamada, Po-Hung Wang, Kanta Hosokawa, Raika Yamagiwa, Kimi Matsumoto, Shoko Ishii, Takaharu Mori, Kiyoshi Yagi, Hitomi Sawai, Hiroyuki Arai, Hiroshi Sugimoto, Yuji Sugita, Yoshitsugu Shiro, Takehiko Tosha
  Proceedings of the National Academy of Sciences 114, 9888–9893,(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
  Journal of Computational Chemistry 38, 2193–2206, (2017).

• Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF
  Arata Furukawa, Kunihito Yoshikaie, Takaharu Mori, Hiroyuki Mori, Yusuke V. Morimoto, Yasunori Sugano, Shigehiro Iwaki, Tohru Minamino, Yuji Sugita, Yoshiki Tanaka, Tomoya Tsukazaki
  Cell Reports 19, 895–901, (2017).

• Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics
  Raimondas Galvelis, Suyong Re, Yuji Sugita
  Journal of Chemical Theory and Computation 13, 1934–1942,(2017).

• Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations
  Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, Florence Tama
  Journal of Computational Chemistry 38, 1447–1461, (2017).

• Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding
  Po-hung Wang, Isseki Yu, Michael Feig, Yuji Sugita
  Chemical Physics Letters 671, 63–70, (2017).

• Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems
  Jaewoon Jung, Yuji Sugita
  Journal of Computational Chemistry 38, 1410–1418, (2017).

2016

• Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
  Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, Michael Feig
  eLife 5, e19274, (2016).

• Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model
  Tadashi Ando, Isseki Yu, Michael Feig, Yuji Sugita
  The Journal of Physical Chemistry B 120, 11856–11865, (2016).

• Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations
  Jaewoon Jung, Akira Naurse, Chigusa Kobayashi, Yuji Sugita
  Journal of Chemical Theory and Computation 12, 4947–4958,(2016).

• Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein
  Yasuhiro Matsunaga, Yasuaki Komuro, Chigusa Kobayashi, Jaewoon Jung, Takaharu Mori, Yuji Sugita
  The Journal of Physical Chemistry Letters 7, 1446–1451, (2016).

• Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms
  Takaharu Mori, Naoyuki Miyashita, Wonpil Im, Michael Feig, Yuji Sugita
  Biochimica et Biophysica Acta - Biomembranes 1858, 1635–1651,(2016).

• Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations
  Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, Yuji Sugita
  Computer Physics Communications 200, 57–65, (2016).

2015

• Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State
  Yoshiki Tanaka, Yasunori Sugano, Mizuki Takemoto, Takaharu Mori, Arata Furukawa, Tsukasa Kusakizako, Kaoru Kumazaki, Ayako Kashima, Ryuichiro Ishitani, Yuji Sugita, Osamu Nureki, Tomoya Tsukazaki
  Cell Reports 13, 1561–1568, (2015).

• Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins
  Chigusa Kobayashi, Yasuhiro Matsunaga, Ryotaro Koike, Motonori Ota, Yuji Sugita
  The Journal of Physical Chemistry B 119, 14584–14593, (2015).

• Replica state exchange metadynamics for improving the convergence of free energy estimates
  Raimondas Galvelis, Yuji Sugita
  Journal of Computational Chemistry 36, 1446–1455, (2015).

• GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
  Jaewoon Jung, Takaharu Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, Yuji Sugita
  Wiley Interdisciplinary Reviews: Computational Molecular Science, 5, 310–323, (2015).

• Sequential data assimilation for single-molecule FRET photon-counting data
  Yasuhiro Matsunaga, Akinori Kidera, Yuji Sugita
  The Journal of Chemical Physics 142, 214115, (2015).

2014

• Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations
  Jaewoon Jung, Takaharu Mori, Yuji Sugita
  Journal of Computational Chemistry 35, 1064–1072, (2014).

2013

• Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems
  Takaharu Mori, Jaewoon Jung, Yuji Sugita
  Journal of Chemical Theory and Computation 9, 5629–5640, (2013).

• Efficient lookup table using a linear function of inverse distance squared
  Jaewoon Jung, Takaharu Mori, Yuji Sugita
  Journal of Computational Chemistry 34, 2412–2420, (2013).