List of works - Yuji Sugita

A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations

scientific article published on 01 July 2020

A weight averaged approach for predicting amide vibrational bands of a sphingomyelin bilayer

scientific article published on 13 October 2015

Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods

scientific article published on 21 November 2011

Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations

article

Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations

article

Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin

scientific article published on 23 July 2021

Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion

scientific article published on 26 October 2020

Author Correction: Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion

scientific article published on 12 November 2020

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

scientific article

CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca(2+)-ATPase.

scientific article published on September 2014

CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations

scientific article published on 28 October 2020

Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments

scientific article published on 27 June 2018

Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase

scientific article

Chemo-Mechanical Coupling in the Transport Cycle of a Heme ABC Transporter

scientific article published on 16 August 2019

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.

scientific article

Confident identification of isomericN-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography

article

Conformational flexibility of N-glycans in solution studied by REMD simulations

scientific article

Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation

article

Correction to "Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations".

scientific article published on 24 December 2014

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

scientific article published on 30 June 2017

Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State

scientific article

Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus

scientific article

Crystal structure of α5β1 integrin ectodomain: Atomic details of the fibronectin receptor ⬇️

scientific article published on March 26, 2012

Crystal structures of Ca2+-ATPase in various physiological states.

scientific article published in April 2003

De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations

scientific article published on 21 August 2019

Dependence of Protein Stability on the Structure of the Denatured State: Free Energy Calculations of I56V Mutation in Human Lysozyme ⬇️

scientific article published on November 1, 1998

Detection of Sphingomyelin Clusters by Raman Spectroscopy.

scientific article

Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein

scientific article published on 6 April 2016

Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins.

scientific article published on 4 November 2015

Dynamic correlation between pressure-induced protein structural transition and water penetration

scientific article

Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability

scientific article published on February 2016

Dynamics of nitric oxide controlled by protein complex in bacterial system.

scientific article published on 28 August 2017

Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments

scientific article published on 01 January 2019

Efficient Parallel Implementations of QM/MM-REMD (Quantum Mechanical/Molecular Mechanics-Replica-Exchange MD) and Umbrella Sampling: Isomerization of H2O2 in Aqueous Solution

scientific article published on 21 June 2013

Efficient lookup table using a linear function of inverse distance squared.

scientific article

Energetics of the Presequence-Binding Poses in Mitochondrial Protein Import Through Tom20 ⬇️

scientific article published on March 5, 2013

Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics

scientific article published on 11 April 2017

Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling

scientific article published on 29 December 2020

Faces of Contemporary CryoEM Information and Modeling

scientific article published on 01 May 2020

Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations.

scientific article

Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations

scientific article published on 01 August 2018

Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T

scientific article published on 27 March 2020

Free energy calculations for DNA base stacking by replica-exchange umbrella sampling

Free-energy function based on an all-atom model for proteins

scientific article published on 01 December 2009

Free-energy function for discriminating the native fold of a protein from misfolded decoys

scientific article

Frontiers in CryoEM Modeling

scientific article published on 13 June 2019

Functionality mapping on internal surfaces of multidrug transporter AcrB based on molecular theory of solvation: implications for drug efflux pathway.

scientific article

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

scientific article

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

scientific article

Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation.

scientific article

Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations

scientific article published on 15 September 2016

Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step

scientific article published on 01 December 2020

Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca²⁺-ATPase.

scientific article

High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations

scientific article published on 27 June 2018

Hydrophobic Core Formation and Dehydration in Protein Folding Studied by Generalized-Ensemble Simulations ⬇️

scientific article published on September 8, 2010

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

scientific article published on 05 April 2022

Implicit Micelle Model for Membrane Proteins Using Superellipsoid Approximation

scientific article published on 09 December 2019

Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations ⬇️

scientific article published on January 28, 2013

Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins.

scientific article

Interionic hydration structures of NaCl in aqueous solution: a combined study of quantum mechanical cluster calculations and QM/EFP-MD simulations.

scientific article published on 27 December 2012

Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation

scientific article published on 01 April 2018

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning.

scientific article

Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

scientific article

MOLECULAR DYNAMICS SIMULATIONS OF DNA DIMERS BASED ON REPLICA-EXCHANGE UMBRELLA SAMPLING II: FREE ENERGY ANALYSIS

article

Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter.

scientific article

Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study

scientific article

Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations.

scientific article

Modeling of the inhibitory interaction of phospholamban with the Ca2+ ATPase.

scientific article

Modeling the Transition State of Enzyme-catalyzed Phosphoryl Transfer Reaction Using QM/MM Method

scientific article published on 01 January 2011

Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions

scientific article published in 2022

Molecular Mechanisms Underlying the Early Stage of Protein Translocation through the Sec Translocon

scientific article published on 01 February 2010

Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides

Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis

scientific article published on 25 February 2020

Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations.

scientific article published on 5 December 2014

Multidimensional replica-exchange method for free-energy calculations

Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems

scientific article

Møller-Plesset perturbation theory gradient in the generalized hybrid orbital quantum mechanical and molecular mechanical method.

scientific article published in February 2010

Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.

scientific article published on 24 April 2017

New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems

scientific article published on 16 November 2020

Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step

article

Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems

scientific article published on 17 July 2021

Population Shift Mechanism for Partial Agonism of AMPA Receptor

scientific article published on 29 November 2018

Protein crowding affects hydration structure and dynamics.

scientific article published on 2 March 2012

Protein folding intermediates on the dimensionality reduced landscape with UMAP and native contact likelihood

scientific article published in 2022

Protein folding simulations by generalized-ensemble algorithms.

scientific article published on January 2014

Protonation of the acidic residues in the transmembrane cation-binding sites of the ca(2+) pump.

scientific article

Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.

scientific article published on 22 December 2015

Reaching new levels of realism in modeling biological macromolecules in cellular environments

scientific article published on 28 August 2013

Reduced native state stability in crowded cellular environment due to protein-protein interactions

scientific article

Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories

article

Relationship between Ca2+-affinity and shielding of bulk water in the Ca2+-pump from molecular dynamics simulations ⬇️

scientific article published on November 23, 2010

Replica state exchange metadynamics for improving the convergence of free energy estimates.

scientific article published on 19 May 2015

Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules

scientific article published on 27 September 2019

Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

Role of the N-Terminal Transmembrane Helix Contacts in the Activation of FGFR3

scientific article published on 05 December 2019

Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations.

scientific article published on 6 December 2013

Sarcolipin regulates sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) by binding to transmembrane helices alone or in association with phospholamban

scientific article

Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations

scientific article published on 17 April 2019

Sequential data assimilation for single-molecule FRET photon-counting data.

scientific article

Short disordered protein segment regulates cross-species transmission of a yeast prion

scientific article published on 13 April 2020

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.

scientific article published on 20 November 2017

Solvent electronic polarization effects on Na(+)-Na(+) and Cl(-)-Cl(-) pair associations in aqueous solution.

scientific article published on 25 July 2013

Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms

scientific article published on 06 November 2019

Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT

scientific article

Structural basis of Sec-independent membrane protein insertion by YidC.

scientific article published on 16 April 2014

Structural basis of ion pumping by Ca(2+)-ATPase of sarcoplasmic reticulum.

scientific article published on November 2003

Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: a molecular dynamics study.

scientific article published on October 2006

Structural diversity and changes in conformational equilibria of biantennary complex-type N-glycans in water revealed by replica-exchange molecular dynamics simulation.

scientific article published on 15 November 2011

Structure of APP-C991-99 and implications for role of extra-membrane domains in function and oligomerization.

scientific article published on 24 April 2018

Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems.

scientific article published on 27 November 2013

The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein

scientific article published on 24 March 2022

The intertransmembrane region of Kaposi's sarcoma-associated herpesvirus modulator of immune recognition 2 contributes to B7-2 downregulation.

scientific article

Theoretical study of magnesium fluoride in aqueous solution.

scientific article published on 17 August 2011

Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.

scientific article published on 31 October 2016

Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations

scientific article published on March 2009

Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF.

scientific article

Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding

scientific article published on 12 December 2011

Weight-Averaged Anharmonic Vibrational Analysis of Hydration Structures of Polyamide 6.

scientific article published on 9 June 2017

List of works by Yuji Sugita

A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations

A weight averaged approach for predicting amide vibrational bands of a sphingomyelin bilayer

Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods

Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations

Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations

Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin

Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion

Author Correction: Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca(2+)-ATPase.

CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations

Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments

Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase

Chemo-Mechanical Coupling in the Transport Cycle of a Heme ABC Transporter

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.

Confident identification of isomericN-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography

Conformational flexibility of N-glycans in solution studied by REMD simulations

Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation

Correction to "Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations".

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State

Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus

Crystal structure of α5β1 integrin ectodomain: Atomic details of the fibronectin receptor ⬇️

Crystal structures of Ca2+-ATPase in various physiological states.

De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations

Dependence of Protein Stability on the Structure of the Denatured State: Free Energy Calculations of I56V Mutation in Human Lysozyme ⬇️

Detection of Sphingomyelin Clusters by Raman Spectroscopy.

Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein

Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins.

Dynamic correlation between pressure-induced protein structural transition and water penetration

Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability

Dynamics of nitric oxide controlled by protein complex in bacterial system.

Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments

Efficient Parallel Implementations of QM/MM-REMD (Quantum Mechanical/Molecular Mechanics-Replica-Exchange MD) and Umbrella Sampling: Isomerization of H2O2 in Aqueous Solution

Efficient lookup table using a linear function of inverse distance squared.

Energetics of the Presequence-Binding Poses in Mitochondrial Protein Import Through Tom20 ⬇️

Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics

Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling

Faces of Contemporary CryoEM Information and Modeling

Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations.

Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations

Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T

Free energy calculations for DNA base stacking by replica-exchange umbrella sampling

Free-energy function based on an all-atom model for proteins

Free-energy function for discriminating the native fold of a protein from misfolded decoys

Frontiers in CryoEM Modeling

Functionality mapping on internal surfaces of multidrug transporter AcrB based on molecular theory of solvation: implications for drug efflux pathway.

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation.

Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations

Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step

Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca²⁺-ATPase.

High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations

Hydrophobic Core Formation and Dehydration in Protein Folding Studied by Generalized-Ensemble Simulations ⬇️

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

Implicit Micelle Model for Membrane Proteins Using Superellipsoid Approximation

Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations ⬇️

Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins.

Interionic hydration structures of NaCl in aqueous solution: a combined study of quantum mechanical cluster calculations and QM/EFP-MD simulations.

Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning.

Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

MOLECULAR DYNAMICS SIMULATIONS OF DNA DIMERS BASED ON REPLICA-EXCHANGE UMBRELLA SAMPLING II: FREE ENERGY ANALYSIS

Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter.

Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study

Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations.

Modeling of the inhibitory interaction of phospholamban with the Ca2+ ATPase.

Modeling the Transition State of Enzyme-catalyzed Phosphoryl Transfer Reaction Using QM/MM Method

Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions

Molecular Mechanisms Underlying the Early Stage of Protein Translocation through the Sec Translocon

Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides

Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis

Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations.

Multidimensional replica-exchange method for free-energy calculations

Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems

Møller-Plesset perturbation theory gradient in the generalized hybrid orbital quantum mechanical and molecular mechanical method.

Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.

New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems