Yuji Sugita

ResearcherID Scopus Author ID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 81

Top Venues

Proceedings of the National Academy of Sciences of the United States of America

The journal of physical chemistry. B

Journal of chemical theory and computation

Journal of chemical information and modeling

Kyoto University (PHD)

This page only lists publications with an associated author ORCID identifier.

Education History

Kyoto University Apr 01 1993 - Mar 31 1998

Japan

PHD :: Department of Chemistry

Publications

Kazuki Watanabe, Qingci Zhao, Ryosuke Iwatsuki, Ryota Fukui, Weitong Ren, Yuji Sugita, Noritaka Nishida
Deciphering the Multi-state Conformational Equilibrium of HDM2 in the Regulation of p53 Binding: Perspectives from Molecular Dynamics Simulation and NMR Analysis. Journal of the American Chemical Society 146 (14) (2024)
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
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. The journal of physical chemistry. B 128 (25) (2024)
Piotr Chyży, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska
Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Piotr Chyży, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska
Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Jaewoon Jung, Cheng Tan, Yuji Sugita
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nature communications 15 (1) (2024)
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
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. The journal of physical chemistry. B (2024)
Kazuki Watanabe, Qingci Zhao, Ryosuke Iwatsuki, Ryota Fukui, Weitong Ren, Yuji Sugita, Noritaka Nishida
Deciphering the Multi-state Conformational Equilibrium of HDM2 in the Regulation of p53 Binding: Perspectives from Molecular Dynamics Simulation and NMR Analysis. Journal of the American Chemical Society 146 (14) (2024)
Jaewoon Jung, Cheng Tan, Yuji Sugita
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nature communications 15 (1) (2024)
Kazuki Watanabe, Qingci Zhao, Ryosuke Iwatsuki, Ryota Fukui, Weitong Ren, Yuji Sugita, Noritaka Nishida
Deciphering the Multi-state Conformational Equilibrium of HDM2 in the Regulation of p53 Binding: Perspectives from Molecular Dynamics Simulation and NMR Analysis. Journal of the American Chemical Society (2024)
Piotr Chyży, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska
Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Ryo Nishihara, Hisham M Dokainish, Yoshiki Kihara, Hiroki Ashiba, Yuji Sugita, Ryoji Kurita
Pseudo-Luciferase Activity of the SARS-CoV-2 Spike Protein for Cypridina Luciferin. ACS central science 10 (2) (2024)
Ryo Nishihara, Hisham M Dokainish, Yoshiki Kihara, Hiroki Ashiba, Yuji Sugita, Ryoji Kurita
Pseudo-Luciferase Activity of the SARS-CoV-2 Spike Protein for Cypridina Luciferin. ACS central science 10 (2) (2024)
Piotr Chyży, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska
Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Piotr Chyży, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska
Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
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. The journal of physical chemistry. B 128 (25) (2024)
Hiroki Otaki, Shun-Ichi Ishiuchi, Masaaki Fujii, Yuji Sugita, Kiyoshi Yagi
Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins. Physical chemistry chemical physics : PCCP (2024)
Hiroki Otaki, Shun-Ichi Ishiuchi, Masaaki Fujii, Yuji Sugita, Kiyoshi Yagi
Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins. Physical chemistry chemical physics : PCCP 26 (13) (2024)
Jaewoon Jung, Cheng Tan, Yuji Sugita
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nature communications 15 (1) (2024)
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
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. The journal of physical chemistry. B 128 (25) (2024)
Jaewoon Jung, Cheng Tan, Yuji Sugita
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nature communications 15 (1) (2024)
Ai Niitsu, Yuji Sugita
Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation. Physical chemistry chemical physics : PCCP 25 (5) (2023)
Ai Niitsu, Yuji Sugita
Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation. Physical chemistry chemical physics : PCCP (2023)
Diego Ugarte La Torre, Shoji Takada, Yuji Sugita
Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers. The Journal of chemical physics 159 (7) (2023)
Ai Niitsu, Yuji Sugita
Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation. Physical chemistry chemical physics : PCCP 25 (5) (2023)
Ai Niitsu, Yuji Sugita
Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation. Physical chemistry chemical physics : PCCP 25 (5) (2023)
Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. Journal of computational chemistry (2023)
Shingo Ito, Kiyoshi Yagi, Yuji Sugita
Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding. The Journal of chemical physics 158 (11) (2023)
Cheng Tan, Ai Niitsu, Yuji Sugita
Highly Charged Proteins and Their Repulsive Interactions Antagonize Biomolecular Condensation. JACS Au 3 (3) (2023)
Isseki Yu, Takaharu Mori, Daisuke Matsuoka, Donatas Surblys, Yuji Sugita
SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations. Journal of computational chemistry (2023)
Mao Oide, Yuji Sugita
Protein folding intermediates on the dimensionality reduced landscape with UMAP and native contact likelihood. The Journal of chemical physics 157 (7) (2022)
George A Pantelopulos, Daisuke Matsuoka, James M Hutchison, Charles R Sanders, Yuji Sugita, John E Straub, D Thirumalai
Formation of extramembrane β -strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
George A Pantelopulos, Daisuke Matsuoka, James M Hutchison, Charles R Sanders, Yuji Sugita, John E Straub, D Thirumalai
Formation of extramembrane β -strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
George A Pantelopulos, Daisuke Matsuoka, James M Hutchison, Charles R Sanders, Yuji Sugita, John E Straub, D Thirumalai
Formation of extramembrane β -strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
George A Pantelopulos, Daisuke Matsuoka, James M Hutchison, Charles R Sanders, Yuji Sugita, John E Straub, D Thirumalai
Formation of extramembrane β -strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
Shingo Ito, Kiyoshi Yagi, Yuji Sugita
Computational Analysis on the Allostery of Tryptophan Synthase: Relationship between α/β-Ligand Binding and Distal Domain Closure. The journal of physical chemistry. B 126 (17) (2022)
Daiki Matsubara, Kento Kasahara, Hisham M Dokainish, Hiraku Oshima, Yuji Sugita
Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions. Molecules (Basel, Switzerland) 27 (17) (2022)
Hiraku Oshima, Yuji Sugita
Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions. Journal of chemical information and modeling 62 (11) (2022)
Yasuhiro Matsunaga, Motoshi Kamiya, Hiraku Oshima, Jaewoon Jung, Shingo Ito, Yuji Sugita
Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation. Biophysical reviews 14 (6) (2022)
Yasuhiro Matsunaga, Motoshi Kamiya, Hiraku Oshima, Jaewoon Jung, Shingo Ito, Yuji Sugita
Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation. Biophysical reviews 14 (6) (2022)
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 computational biology 18 (4) (2022)
George A Pantelopulos, Daisuke Matsuoka, James M Hutchison, Charles R Sanders, Yuji Sugita, John E Straub, D Thirumalai
Formation of extramembrane β -strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
Hisham M Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung, Yuji Sugita
The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein. eLife 11 (2022)
Keisuke Fujiyama, Naoki Kato, Suyong Re, Kiyomi Kinugasa, Kohei Watanabe, Ryo Takita, Toshihiko Nogawa, Tomoya Hino, Hiroyuki Osada, Yuji Sugita, Shunji Takahashi, Shingo Nagano
Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*. Angewandte Chemie (International ed. in English) 60 (41) (2021)
Kiyoshi Yagi, Yuji Sugita
Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin. Journal of chemical theory and computation 17 (8) (2021)
Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie Elizabeth Amaro
Faces of Contemporary CryoEM Information and Modeling. Journal of chemical information and modeling 60 (5) (2021)
Chigusa Kobayashi, Yasuhiro Matsunaga, Jaewoon Jung, Yuji Sugita
Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca2+-ATPase. Proceedings of the National Academy of Sciences of the United States of America 118 (40) (2021)
Kento Kasahara, Suyong Re, Grzegorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Miyata-Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael F Feig, Yuji Sugita
Reduced efficacy of a Src kinase inhibitor in crowded protein solution. Nature communications 12 (1) (2021)
Weitong Ren, Hisham M Dokainish, Ai Shinobu, Hiraku Oshima, Yuji Sugita
Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations. The journal of physical chemistry. B 125 (11) (2021)
Jaewoon Jung, Kento Kasahara, Chigusa Kobayashi, Hiraku Oshima, Takaharu Mori, Yuji Sugita
Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems. Journal of chemical theory and computation 17 (8) (2021)
Jaewoon Jung, Yuji Sugita
Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step. The Journal of chemical physics 153 (23) (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. Journal of chemical information and modeling 61 (7) (2021)
Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, Yuji Sugita
Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins. Journal of chemical information and modeling 61 (5) (2021)
Daisuke Fujinami, Hajime Motomura, Hiraku Oshima, Abdullah-Al- Mahin, Khaled M Elsayed, Takeshi Zendo, Yuji Sugita, Kenji Sonomoto, Daisuke Kohda
Correction to "Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis". The journal of physical chemistry letters 12 (44) (2021)
Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations. The Journal of chemical physics 153 (4) (2021)
Kiyoshi Yagi, Shingo Ito, Yuji Sugita
Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations. The journal of physical chemistry. B 125 (18) (2021)
Hiraku Oshima, Suyong Re, Yuji Sugita
Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method. Journal of chemical information and modeling 60 (11) (2020)
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. Journal of computational chemistry 42 (4) (2020)
Seonghoon Kim, Hiraku Oshima, Han Zhang, Nathan R Kern, Suyong Re, Jumin Lee, Benoı T Roux, Yuji Sugita, Wei Jiang, Wonpil Im
CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations. Journal of chemical theory and computation 16 (11) (2020)
Kazuaki Matoba, Tetsuya Kotani, Akihisa Tsutsumi, Takuma Tsuji, Takaharu Mori, Daisuke Noshiro, Yuji Sugita, Norimichi Nomura, So Iwata, Yoshinori Ohsumi, Toyoshi Fujimoto, Hitoshi Nakatogawa, Masahide Kikkawa, Nobuo N Noda
Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion. Nature structural & molecular biology 27 (12) (2020)
Daisuke Fujinami, Hajime Motomura, Hiraku Oshima, Abdullah-Al- Mahin, Khaled M Elsayed, Takeshi Zendo, Yuji Sugita, Kenji Sonomoto, Daisuke Kohda
Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis. The journal of physical chemistry letters 11 (5) (2020)
Koichi Tamura, Yuji Sugita
Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T. The journal of physical chemistry letters 11 (8) (2020)
Toshinobu Shida, Yuji O Kamatari, Takao Yoda, Yoshiki Yamaguchi, Michael Feig, Yumiko Ohhashi, Yuji Sugita, Kazuo Kuwata, Motomasa Tanaka
Short disordered protein segment regulates cross-species transmission of a yeast prion. Nature chemical biology 16 (7) (2020)
Hisham M Dokainish, Yuji Sugita
Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling. International journal of molecular sciences 22 (1) (2020)
Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie Elizabeth Amaro
Frontiers in CryoEM Modeling. Journal of chemical information and modeling 59 (7) (2019)
Kiyoshi Yagi, Kenta Yamada, Chigusa Kobayashi, Yuji Sugita
Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations. Journal of chemical theory and computation 15 (3) (2019)
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
Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations. Journal of computational chemistry 40 (21) (2019)
Takaharu Mori, Yuji Sugita
Implicit Micelle Model for Membrane Proteins Using Superellipsoid Approximation. Journal of chemical theory and computation 16 (1) (2019)
Ai Niitsu, Suyong Re, Hiraku Oshima, Motoshi Kamiya, Yuji Sugita
De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations. Journal of chemical information and modeling 59 (9) (2019)
Kimiko Kuroki, Haruki Matsubara, Ryo Kanda, Naoyuki Miyashita, Mitsunori Shiroishi, Yuko Fukunaga, Jun Kamishikiryo, Atsushi Fukunaga, Hideo Fukuhara, Kaoru Hirose, Joan S Hunt, Yuji Sugita, Shunsuke Kita, Toyoyuki Ose, Katsumi Maenaka
Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms. Journal of immunology (Baltimore, Md. : 1950) 203 (12) (2019)
Koichi Tamura, Hiroshi Sugimoto, Yoshitsugu Shiro, Yuji Sugita
Chemo-Mechanical Coupling in the Transport Cycle of a Heme ABC Transporter. The journal of physical chemistry. B 123 (34) (2019)
Hiraku Oshima, Suyong Re, Yuji Sugita
Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules. Journal of chemical theory and computation 15 (10) (2019)
Daisuke Matsuoka, Motoshi Kamiya, Takeshi Sato, Yuji Sugita
Role of the N-Terminal Transmembrane Helix Contacts in the Activation of FGFR3. Journal of computational chemistry 41 (6) (2019)
Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step. Journal of chemical theory and computation 15 (1) (2018)
Suyong Re, Shigehisa Watabe, Wataru Nishima, Eiro Muneyuki, Yoshiki Yamaguchi, Alexander D MacKerell, Yuji Sugita
Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase. Scientific reports 8 (1) (2018)
Yasuhiro Matsunaga, Yuji Sugita
Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning. eLife 7 (2018)
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. Journal of computational chemistry 38 (25) (2017)
Bo Thomsen, Tomonori Kawakami, Isamu Shigemoto, Yuji Sugita, Kiyoshi Yagi
Weight-Averaged Anharmonic Vibrational Analysis of Hydration Structures of Polyamide 6. The journal of physical chemistry. B 121 (24) (2017)
Raimondas Galvelis, Yuji Sugita
Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics. Journal of chemical theory and computation 13 (6) (2017)
Michael F Feig, Isseki Yu, Po-Hung Wang, Grzegorz Nawrocki, Yuji Sugita
Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. The journal of physical chemistry. B 121 (34) (2017)
Raimondas Galvelis, Suyong Re, Yuji Sugita
Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics. Journal of chemical theory and computation 13 (5) (2017)
Grzegorz Nawrocki, Po-Hung Wang, Isseki Yu, Yuji Sugita, Michael F Feig
Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation. The journal of physical chemistry. B 121 (49) (2017)

Yuji Sugita.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Yuji Sugita