GENESIS papers

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).

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).

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).


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).

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, (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).


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).

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


2018

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, (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).


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).

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, (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).