Yuji Sugita
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Chemistry Physics
Yuji Sugita's Degrees
- PhD Chemistry University of Tokyo
- Masters Chemistry University of Tokyo
- Bachelors Chemistry University of Tokyo
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(Suggest an Edit or Addition)Yuji Sugita's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Replica-exchange molecular dynamics method for protein folding (1999) (3573)
- Multidimensional replica-exchange method for free-energy calculations (2000) (713)
- Generalized-ensemble algorithms for molecular simulations of biopolymers. (2000) (680)
- Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape (2000) (248)
- Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+). (2005) (233)
- Conformational transition of Sec machinery inferred from bacterial SecYE structures (2008) (230)
- Structural basis of ion pumping by Ca2+‐ATPase of sarcoplasmic reticulum (2003) (215)
- Crystal structure of α5β1 integrin ectodomain: Atomic details of the fibronectin receptor (2012) (197)
- Modeling of the inhibitory interaction of phospholamban with the Ca2+ ATPase (2003) (192)
- Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm (2016) (188)
- Structural basis of Sec-independent membrane protein insertion by YidC (2014) (186)
- Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT (2013) (172)
- Protein crowding affects hydration structure and dynamics. (2012) (167)
- Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion (2020) (165)
- Sarcolipin regulates sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) by binding to transmembrane helices alone or in association with phospholamban (2003) (157)
- GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations (2015) (137)
- Comparisons of force fields for proteins by generalized-ensemble simulations (2004) (133)
- Reduced native state stability in crowded cellular environment due to protein-protein interactions. (2013) (128)
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations (2017) (118)
- Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding. (2012) (117)
- Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test (2003) (108)
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. (2016) (104)
- Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus (2012) (100)
- Structural basis of ion pumping by Ca(2+)-ATPase of sarcoplasmic reticulum. (2003) (99)
- GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms (2017) (98)
- Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations (2004) (82)
- Inaugural Article: Structural role of countertransport revealed in Ca2+ pump crystal structure in the absence of Ca2+. (2005) (80)
- Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. (2009) (77)
- Effect of bisecting GlcNAc and core fucosylation on conformational properties of biantennary complex-type N-glycans in solution. (2012) (75)
- Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation. (2017) (73)
- Crystal Structures of Ca2+‐ATPase in Various Physiological States (2003) (70)
- Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system (2003) (68)
- Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State. (2015) (62)
- Free energy calculations for DNA base stacking by replica-exchange umbrella sampling (2004) (61)
- Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations (2019) (61)
- Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study (2008) (60)
- Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability. (2016) (59)
- Dynamic correlation between pressure-induced protein structural transition and water penetration. (2010) (58)
- Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology. (2015) (58)
- Reaching new levels of realism in modeling biological macromolecules in cellular environments. (2013) (57)
- Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations. (2014) (53)
- Protonation of the acidic residues in the transmembrane cation-binding sites of the ca(2+) pump. (2005) (52)
- Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations. (2018) (51)
- Rapid flip-flop motions of diacylglycerol and ceramide in phospholipid bilayers (2012) (49)
- Cooperative folding mechanism of a β‐hairpin peptide studied by a multicanonical replica‐exchange molecular dynamics simulation (2006) (49)
- Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics. (2017) (48)
- CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations. (2020) (45)
- Confident identification of isomeric N-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography. (2012) (45)
- Ab initio replica-exchange Monte Carlo method for cluster studies (2001) (44)
- Replica-exchange umbrella sampling combined with Gaussian accelerated molecular dynamics for free-energy calculation of biomolecules. (2019) (42)
- Functionality mapping on internal surfaces of multidrug transporter AcrB based on molecular theory of solvation: implications for drug efflux pathway. (2011) (41)
- Interionic hydration structures of NaCl in aqueous solution: a combined study of quantum mechanical cluster calculations and QM/EFP-MD simulations. (2013) (39)
- Flexible fitting to cryo‐EM density map using ensemble molecular dynamics simulations (2017) (39)
- Structural diversity and changes in conformational equilibria of biantennary complex-type N-glycans in water revealed by replica-exchange molecular dynamics simulation. (2011) (38)
- Physical basis for characterizing native structures of proteins (2007) (37)
- Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF. (2017) (37)
- Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems. (2013) (36)
- Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations. (2010) (36)
- Conformational flexibility of N-glycans in solution studied by REMD simulations (2012) (35)
- Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A (1998) (34)
- Analysis of lipid surface area in protein–membrane systems combining voronoi tessellation and monte carlo integration methods (2012) (33)
- Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein (2021) (33)
- Free‐energy function based on an all‐atom model for proteins (2009) (33)
- Multidimensional umbrella sampling and replica‐exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers (2014) (32)
- Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape (2019) (32)
- Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning (2018) (31)
- Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending (2019) (31)
- Whole-Cell Models and Simulations in Molecular Detail. (2019) (31)
- Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding (2017) (31)
- Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase (2012) (31)
- Detection of Sphingomyelin Clusters by Raman Spectroscopy. (2016) (30)
- Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: a molecular dynamics study. (2006) (30)
- Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms (2001) (30)
- Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent. (2005) (29)
- Structures of a peptide fragment of β2‐microglobulin studied by replica‐exchange molecular dynamics simulations – Towards the understanding of the mechanism of amyloid formation (2005) (28)
- Free‐energy function for discriminating the native fold of a protein from misfolded decoys (2011) (27)
- Relationship between Ca2+-affinity and shielding of bulk water in the Ca2+-pump from molecular dynamics simulations (2010) (27)
- Dynamics of nitric oxide controlled by protein complex in bacterial system (2017) (25)
- Structure of APP-C991-99 and implications for role of extra-membrane domains in function and oligomerization. (2018) (25)
- Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms (2019) (25)
- Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein. (2016) (23)
- New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals (2007) (23)
- Quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) study on intra-molecular proton transfer of glycine in water (2012) (23)
- Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments. (2019) (21)
- Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations (2019) (21)
- Efficient parallel implementations of QM/MM-REMD (quantum mechanical/molecular mechanics-replica-exchange MD) and umbrella sampling: isomerization of H2O2 in aqueous solution. (2013) (21)
- Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations (2016) (21)
- Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations (2014) (20)
- Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations. (2016) (20)
- Replica-Exchange Monte Carlo Method for Ar Fluid (2000) (20)
- Efficient lookup table using a linear function of inverse distance squared (2013) (20)
- How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme. (2003) (20)
- Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase (2018) (19)
- Solvent electronic polarization effects on Na(+)-Na(+) and Cl(-)-Cl(-) pair associations in aqueous solution. (2013) (19)
- Dependence of protein stability on the structure of the denatured state: free energy calculations of I56V mutation in human lysozyme. (1998) (19)
- Replica state exchange metadynamics for improving the convergence of free energy estimates (2015) (18)
- Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method (2020) (18)
- Molecular mechanisms underlying the early stage of protein translocation through the Sec translocon. (2010) (18)
- New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems (2020) (18)
- Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model. (2016) (18)
- Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments (2018) (18)
- De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations (2019) (17)
- Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter. (2016) (16)
- Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations. (2021) (15)
- Reduced efficacy of a Src kinase inhibitor in crowded protein solution (2020) (14)
- Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation. (2018) (14)
- Sequential data assimilation for single-molecule FRET photon-counting data. (2015) (13)
- The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein (2021) (13)
- Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics. (2017) (13)
- Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning. (2019) (13)
- Computational analysis of thermal stability: effect of Ile-->Val mutations in human lysozyme. (1998) (13)
- Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins. (2015) (12)
- The Intertransmembrane Region of Kaposi's Sarcoma-Associated Herpesvirus Modulator of Immune Recognition 2 Contributes to B7-2 Downregulation (2012) (12)
- Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories. (2018) (12)
- Water Orientation at Ceramide/Water Interfaces Studied by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulation (2016) (12)
- Energetics of the presequence-binding poses in mitochondrial protein import through Tom20. (2013) (12)
- Amide A band is a fingerprint for water dynamics in reverse osmosis polyamide membranes (2020) (12)
- Use of single-molecule time-series data for refining conformational dynamics in molecular simulations. (2020) (11)
- Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations (2021) (11)
- Theoretical study of magnesium fluoride in aqueous solution. (2011) (11)
- Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution (2021) (10)
- Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems. (2021) (10)
- Weight-Averaged Anharmonic Vibrational Analysis of Hydration Structures of Polyamide 6. (2017) (10)
- CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca(2+)-ATPase. (2014) (10)
- Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step. (2018) (9)
- Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data (2011) (9)
- Rational design of crystal contact‐free space in protein crystals for analyzing spatial distribution of motions within protein molecules (2016) (9)
- Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations. (2013) (9)
- A weight averaged approach for predicting amide vibrational bands of a sphingomyelin bilayer. (2015) (9)
- Møller-Plesset perturbation theory gradient in the generalized hybrid orbital quantum mechanical and molecular mechanical method. (2010) (9)
- An Analysis on Protein Folding Problem by Replica-Exchange Method (2000) (8)
- Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step. (2020) (8)
- Short disordered protein segment regulates cross-species transmission of a yeast prion (2020) (8)
- Replica-Exchange Methods for Biomolecular Simulations. (2019) (8)
- Effects of the fixed end in single-molecule imaging techniques: A replica-exchange molecular dynamics simulation study (2005) (8)
- Generalized-ensemble algorithms for protein folding simulations (2007) (8)
- A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase (2009) (8)
- MOLECULAR DYNAMICS SIMULATIONS OF DNA DIMERS BASED ON REPLICA-EXCHANGE UMBRELLA SAMPLING I: TEST OF SAMPLING EFFICIENCY (2005) (8)
- Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T. (2020) (8)
- Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation (2011) (8)
- Protein assembly and crowding simulations. (2022) (7)
- Protein folding simulations by generalized-ensemble algorithms. (2014) (7)
- Generalized-ensemble simulations of spin systems and protein systems (2001) (7)
- Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling (2020) (7)
- Implicit micelle model for membrane proteins using super-ellipsoid approximation. (2019) (7)
- Hierarchical domain‐motion analysis of conformational changes in sarcoplasmic reticulum Ca2+‐ATPase (2015) (7)
- Replica-exchange molecular dynamics simulation of diffracted X-ray tracking (2007) (7)
- Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-specific NMR Thermodynamic Analysis. (2020) (7)
- Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca2+-ATPase (2021) (6)
- Recent Applications of Replica-Exchange Molecular Dynamics Simulations of Biomolecules (2012) (6)
- Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations. (2016) (6)
- High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations (2018) (6)
- Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides (2018) (6)
- Salt effects on hydrophobic‐core formation in folding of a helical miniprotein studied by molecular dynamics simulations (2014) (5)
- Chemo-Mechanical Coupling in the Transport Cycle of a Heme ABC Transporter. (2019) (5)
- Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps (2021) (5)
- Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons (2021) (5)
- Free energy calculations of the stacked and unstacked states for DNA dimers by replica‐exchange umbrella sampling (2004) (5)
- Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins (2010) (5)
- Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection (2021) (4)
- Chapter 14. All-atom Molecular Dynamics Simulation of Proteins in Crowded Environments (2019) (4)
- A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations. (2020) (4)
- Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin. (2021) (4)
- MOLECULAR DYNAMICS SIMULATIONS OF DNA DIMERS BASED ON REPLICA-EXCHANGE UMBRELLA SAMPLING II: FREE ENERGY ANALYSIS (2005) (4)
- Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems (2017) (4)
- Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations. (2021) (4)
- Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions (2022) (3)
- Author Correction: Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion (2020) (3)
- Free-energy landscapes of proteins in solution by generalized-ensemble simulations. (2009) (3)
- Amino acid activation analysis of primitive aminoacyl-tRNA synthetases encoded by both strands of a single gene using the malachite green assay (2021) (3)
- Population Shift Mechanism for Partial Agonism of AMPA Receptor. (2019) (3)
- Structural Mechanisms Underlying Activity Changes in an AMPA-type Glutamate Receptor Induced by Substitutions in Its Ligand-Binding Domain. (2019) (3)
- Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance Ratio (2019) (3)
- Role of the N‐Terminal Transmembrane Helix Contacts in the Activation of FGFR3 (2019) (3)
- Structural effects of spike protein D614G mutation in SARS-CoV-2 (2022) (3)
- Structure of APP-C991-99 and Implications for Role of Extra-Membrane Domains in Function and Oligomerization (2018) (3)
- REIN: Replica‐exchange INterface for simulating protein dynamics and function (2015) (3)
- 1P-037 Mg^ -sensing mechanism of Mg^ transporter MgtE probed by molecular dynamics study(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (3)
- Weight Averaged Anharmonic Vibrational Calculations: Applications to Polypeptide, Lipid Bilayers, and Polymer Materials (2019) (3)
- Molecular Dynamics Simulations of Biomolecules in Cellular Environments (2017) (2)
- [Structure and functions of a calcium pump]. (2005) (2)
- Protein folding intermediates on the dimensionality reduced landscape with UMAP and native contact likelihood. (2022) (2)
- Surface-Tension Replica-Exchange Molecular Dynamics Method for Efficient Conformational Sampling of Biological Membrane Systems (2014) (2)
- Frontiers in CryoEM Modeling (2019) (2)
- Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins (2021) (2)
- Implicit micelle model for membrane proteins using super-ellipsoid approximation (2019) (2)
- Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation (2022) (2)
- Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images (2022) (2)
- Acceleration of Classical Molecular Dynamics Simulations (2019) (2)
- Molecular Dynamics Simulation of Glycans (2020) (2)
- Flip-Flop Motions of Lipid Molecules in Mixed Bilayer Systems (2010) (1)
- Computational Analysis on the Allostery of Tryptophan Synthase: Relationship between α/β-Ligand Binding and Distal Domain Closure (2022) (1)
- Computer simulations of proton transfer in cytochrome c oxidase and nitric oxide reductase (2010) (1)
- Correction to "Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations". (2015) (1)
- Replica-Exchange Molecular Dynamics Simulations of Amyloid Precursor Protein Dimer in Membrane (2010) (1)
- Site of Biosynthesis of Tyrosinase in Mammalian Melanocyte (1981) (1)
- Formation of extramembrane β-strands controls dimerization of transmembrane helices in amyloid precursor protein C99. (2022) (1)
- Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics (2022) (1)
- Integrative Modeling of Protein Dynamics from Time-Series Data of Single-Molecule Experiments and Molecular Dynamics Simulations (2019) (1)
- Drug Extrusion Process of Mate Multidrug Efflux Transporter Revealed by Molecular Dynamics Simulations (2014) (1)
- 3P-031 Molecular dynamics simulation studies on the differences in the binding mechanism of LILRB1/HLA-G and LILRB2/HLA-G(Protein:Structure & Function,The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (1)
- Protein-Protein Interactions in Crowded Cellular Environments (2012) (1)
- [Structural and functional relationships in Ca2+-pump]. (2008) (1)
- Multiple sub-state structures of SERCA2b reveal conformational overlap at transition steps during the catalytic cycle. (2022) (1)
- Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions (2022) (1)
- Faces of Contemporary CryoEM Information and Modeling (2020) (1)
- Weight average approaches for predicting dynamical properties of biomolecules. (2021) (1)
- 2P072 Efficient Lookup Table using a Linear Function of Inverse Distance Squared(01D. Protein: Function,Poster) (2013) (0)
- 30aPS-130 Dynamics of lipid molecules in membrane systems (2009) (0)
- Chemo-mechanical Coupling in the Transport Cycle of a Type II ABC Transporter (2018) (0)
- Acceleration of residue-level coarse-grained molecular dynamics by efficient parallelization. (2023) (0)
- Generalized ensemble simulation of protein G in model solvent (2001) (0)
- Effects of T686A Mutation on the Structural Stability of the AMPA Receptor Ligand-Binding Domain (2018) (0)
- 1P100 Comparison of the predicted structure of the FGFR3 transmembrane domain by enhanced sampling simulations with experimental results(03. Membrane proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- Computational Investigation of the Hydration of the H Channel of Bovine Heart Cytochrome c Oxidase (2018) (0)
- 2P041 Molecular dynamics simulations of the conformational transitions involved in the enzymatic cycle of a reversible phosphorylation(The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- 3P314 Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulations(30.Miscellaneous topics,Poster,The 51st Annual Meeting of the Biophysical Society of Japan) (2013) (0)
- Visualization of the interfacial electrostatic complementarity: A method for analysis of protein-protein interaction based on fragment molecular orbital method (2021) (0)
- Computer Simulations of Protein Folding by New Generalize-Ensemble Algorithms (2001) (0)
- Hidden Markov Modeling of Molecular Orientations and Structures from High-Speed Atomic Force Microscopy Time-Series Images (2022) (0)
- Non Local Interactions are Essential Elements of the Initiation and Guidance of the Folding Pathway of Proteins (2014) (0)
- 2P202 Probing the sphingomyelin clusters in pure and mix lipid bilayer by the Raman spectroscopy : A theoretical study(13A. Biological & Artificial membrane:Structure & Property,Poster) (2014) (0)
- Unraveling SARS-CoV-2 spike protein activation pathway reveals unprecedented cryptic pockets (2022) (0)
- 2P208 Study on sphingomyelin aggregates in model membranes by Raman spectroscopy(13A. Biological & Artificial membrane:Structure & Property,Poster) (2014) (0)
- 3P-087 Molecular Dynamics Study of the SecY Protein-conducting Channel(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- 3P084 β-Hairpin Structures of G-peptide in Water Studied by a Molecular Dynamics Simulation (2004) (0)
- 3C1148 New implementation of the reaction path determination in the QM/MM method(3C Protein: Funcrion 2,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- Tackling a novel coronavirus at Fugaku (2020) (0)
- 1P105 The function of the proton-counter transport in Ca^ ATPase of sarcoplasmic reticulm (2004) (0)
- Folding Simulation of a Mini Protein with a Hydrophobic Core and α-helices (2012) (0)
- Tertiary Structure Prediction of Peptides in Aqueous Soution. (1999) (0)
- Correction to "Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis". (2021) (0)
- Conformational Diversity of N-Glycans in Solution Studied by REMD Simulations (2013) (0)
- 3P067 Folding simulations of a small helical protein by multicanonical replica-exchange method(Protein: Property,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- [Structure and function of hemoglobin (author's transl)]. (1978) (0)
- Molecular Dynamics Simulations of a Riboswitch Binding Aminoglycoside Antibiotics (2018) (0)
- Issue Information (2019) (0)
- 3PT157 Surface tension replica exchange molecular dynamics method for an efficient sampling of lipid bilayer structures(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- All-atom Molecular Dynamics Simulations of Proteins and Metabolites under the Crowding Environment in Bacterial Cytoplasm (2015) (0)
- 1P099 A novel method for predicting the native structure of a protein(3. Protein folding and misfolding (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- Dimer Conformation Of Amyloid Precursor Protein Fragments In Membrane (2009) (0)
- New Technologies that Propel Biophysics (2021) (0)
- Effect of Hydrophobic Interactions on Volume and Thermal Expansivity as Derived from Micelle Formation (2013) (0)
- Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. (2023) (0)
- 21aEF-12 The Structure Prediction of APP Dimer and Monomer (2010) (0)
- 2P123 Molecular dynamics simulation of outer mitochondrial membrane protein Tom20-presequence complex(The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- 3E1110 Replica-exchange interface program (REIN)(Proteins:Structure,Oral Presentation) (2012) (0)
- Optimal Temperature and Pressure Evaluations in Molecular Dynamics Simulations with a Large Time Step (2019) (0)
- S11I3 How flexible is the structure of Ca^ -pump in membrane? A molecular dynamics study(Discussion on the mechanisms of energy / signal transductions in the membrane proteins by young researchers) (2007) (0)
- 20P16In silico mutants of nitric oxide reductases provide insights into development of proton pathways in the heme-copper oxidase superfamily (2012) (0)
- Development of an effective conformational-sampling method for a peptide in water by a new generalized-ensemble algorithm (2000) (0)
- 2PT139 Molecular dynamics simulations of SR Ca2+-pump in the ATP bound forms(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- 1P046 Metadynamics : Implementation in GENESIS Software Package and Demonstration of the Efficient Computational Simulations of Biomolecules(01B. Protein:Structure & Function,Poster) (2013) (0)
- Journal Pre-proof Structural Effects of Spike Protein D614G Mutation in SARS-CoV-2 (2022) (0)
- Conformational Fluctuations and Changes of Sr-Ca2+-ATPase on the E1/E2 Transition (2019) (0)
- Repulsive interaction and secondary structure of highly charged proteins in regulating biomolecular condensation (2022) (0)
- 1P043 Fragment-based drug design using the 3D-RISM ligandmapping method : An application to FK506-binding protein(Protein:Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- ALGORITHMS FOR BROWNIAN DYNAMICS SIMULATION (2020) (0)
- Theoretical analyses of the structural stability and function of cd 1 NiR : cNOR complex ○ (2017) (0)
- 3B1022 A computational Investigation into the MHC-I Recognition Mechanism of MIR2 from Kaposi's Sarcoma-Associated Herpesvirus(Proteins:Structure & Function III:Dynamics and Circadian Rhythm,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- 1P105 Molecular dynamics simulations of ATP/ADP bound forms of SR Ca^ -ATPase using CHARMM force field with modified polyphosphate parameters(03. Membrane proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 1P273 Macromolecular dynamics in intracellular environment : Bronian dynamics simulation study(24. Mathematical biology,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 1P216 Surface-tension replica-exchange molecular dynamics simulations of biological membrane systems(13B. Biological & Artificial membrane: Dynamics,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- Generalized‐Ensemble Monte Carlo Algorithms for Simulations of Proteins (2004) (0)
- Binding free energy landscape of c-Src kinase to its inhibitors sampled by molecular dynamics simulations: Effect of ligand size and flexibility. (2023) (0)
- All-Atom Molecular Dynamics Simulation of the Altered Protein-Protein Interaction with Metabolites and Ions in the Cytoplasm (2020) (0)
- Non Linear Effects of Macromolecular Crowding on the Mechanical Unfolding of Proteins (2013) (0)
- Improved Constrained Optimization Method for Reaction-Path Determination in Quantum Mechanical/Molecular Mechanical Calculations (2013) (0)
- 2P056 Simulations of peptide fragments of beta2-microglobulin : towards the understanding of the mechanism of amyloid formations (2004) (0)
- 3P224 Lipid dynamics in mixed bilayer systems with micro domains of cholesterol and diacylglycerol(Biol & Artifi memb.: Dynamics,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- I-B-1 Optimization of Protein Force-Field Parameters with the Protein Data Bank SAKAE, (2005) (0)
- 1P127 Model of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations (2015) (0)
- Flexible Choice of Solute in Replica Exchange with Solute Tempering Can Improve Performance of Conformation Search for Small Proteins (2018) (0)
- 1PT201 Protein stability and dynamics under cellular environments(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- Conformational flexibility of N-glycans in solution studied by REMD simulations (2012) (0)
- Analyses of Structure Changes and Free Energy of Sarco/Endoplasmic Reticulum Ca2+-ATPase (2022) (0)
- 3P109 X 線結晶構造の決定に向けた膜タンパク質構造安定性の理論 的向上 Theoretical Enhancement of Structural Stability of a Membrane Protein for X-ray Crystallography (2014) (0)
- Chapter 9 Computational Biophysics Research Team 9 . 1 Members (2017) (0)
- 1P058 All-Atom Molecular Dynamics Simulation of Bacterial Cytoplasm(01C. Protein:Property,Poster) (2013) (0)
- New implementation of QM/MM methods using modified generalized hybrid orbitals (GHO) (2007) (0)
- 3P044 The development of multi-dimensional replica-exchange molecular dynamics program (REIN)(Protein: Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- 22pEC-8 Dynamic correlation between pressure-induced protein structural transition and water penetration studied by molecular dynamics simulation (2010) (0)
- Molecular dynamics simulations of membrane proteins (2013) (0)
- Multiple Conformers and their Spectroscopic Properties of N-Glycan Predicted using Replica-Exchange Simulations (2013) (0)
- 3P112 Interaction between cholesterol and transmembrane region of Amyloid Precursor Protein(03. Membrane proteins,Poster) (2013) (0)
- 1P073 Development of a free-energy function toward predicting the native structure of a protein(Protein:Property,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- 2P046 Conformational changes of SERCA in response to reactions described by hierarchical domain-motion analysis(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 2P-078 Prediction of equilibrium and dynamic structural properties of membrane proteins(Membrane proteins,The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- Repulsive interactions in regulating biomolecular condensation: A case study on TDP-43 and Hero11. (2023) (0)
- 1P129 Free-energy analysis of the effect of ions on protein structure(07. Water & Hydration & Electrolyte,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 1PT212 Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- 3P111 Molecular dynamics simulations of SR Ca^ -ATPase using improved ATP force field(03. Membrane proteins,Poster) (2013) (0)
- 1P204 Structure and orientation of hydrating water molecules at phospholipid/water interface revealed by molecular dynamics simulation(13A. Biological & Artificial membrane: Structure & Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 1P085 What interactions are important for the stability and specificity of conformations of a β-hairpin peptide (2005) (0)
- Title Tunnel Formation Inferred from the I-Form Structures of theProton-Driven Protein Secretion Motor SecDF (2019) (0)
- 1B1424 P35 Computer Simulations Reveal Proton Transfer Pathways in Nitric Oxide Reductases(Membrane Proteins 1,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- Author response: Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning (2018) (0)
- Theoretical Study of the Influence of Cellular Crowding on the Dynamics and Interactions of Proteins (2016) (0)
- 3P-072 Development of the method reproducing the bulk lipid surface-area in the molecular dynamics simulation of the protein-membrane complex(Protein:Measurement & Analysis,The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- Dynamics and Interactions of Proteins and Metabolites in Cellular Crowding Environments: All-Atom Molecular Dynamics Study of Proteins and Metabolites in Cellular Crowding Environments: All-atom Molecular Dynamics Study (2018) (0)
- Theoretical Enhancement of Structural Stability of a Membrane Protein for X-ray Crystallography (2014) (0)
- 1SK-02 Molecular dynamics simulations for the protein secretory pathway(1SK High Performance Computational Approaches to Biological Functions,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- 2SB1450 Molecular simulations of soft interaction between calcium pump and phospholamban(2SB Intrinsically Disordered Proteins:Structure,Property and Function,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- 3P048 Computer simulations of nitric oxide reductase : proton transfer pathways and mechanisms(Protein: Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- Invited: Atomistic Molecular Dynamics Simulation of a Complete Model of Bacterial Cytoplasm (2015) (0)
- 1A1700 P58 Morphology changes of DAPC/diaylgclyerol membrane systems(Biol & Artifi memb 1: Structure & Property, Dynamics,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- Molecular Dynamics Simulations for Conformational Changes on a Reaction Step of SR-Ca 2+ -ATPase (2018) (0)
- Protein folding pathway and intermediates on the dimensionality reduced landscape with UMAP and native contact likelihood. (2023) (0)
- 3P210 Acceleration of lipid lateral diffusion by generalized-ensemble molecular dynamics simulation(13B. Biological & Artifical membrane: Dynamics,Poster) (2013) (0)
- 1J1700 Comparison of Force Fields by Generalized-Ensemble Simulation of Small Polypeptides (2002) (0)
- [Modeling the transition state of enzyme-catalyzed phosphoryl transfer reaction using QM/MM method]. (2011) (0)
- [Glycophospholipid-linked membrane proteins of human erythrocytes]. (1988) (0)
- 3D0936 Prediction of dynamical conformation of biantennary complex-type N-glycan in water by replica-exchange molecular dynamics simulations(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- Protein Diffusion Around Bacterial Nucleoid (2017) (0)
- Different Scale Conformational Changes of SERCA Analyzed with Motion Tree Method (2013) (0)
- Crystal structure of nitric oxide reductase (2012) (0)
- Author response: Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm (2016) (0)
- 3P091 How lipids interact with calcium pump : A molecular dynamics study (2004) (0)
- [Simple method for making cDNA library]. (1986) (0)
- Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding. (2023) (0)
- Analysis of the area per lipid in protein-membrane systems (2012) (0)
- Intentional crystal-contact-free space in protein crystal (2014) (0)
- Free Energy Analysis on the Tom20-Presequence Complex in Solution for Understanding a Dynamic-Equilibrium Model (2013) (0)
- Voronoi Analysis of Lipid Surface Area in Protein-Membrane Systems (2010) (0)
- Protein Diffusion in a Dense Solution Studied by All-Atom Molecular Dynamics Simulations (2018) (0)
- Replica State Exchange Metadynamics for Improving the Convergence of Free Energy Estimates (2016) (0)
- Structural and functional basis for HLA-G isoform recognition of immune checkpoint receptor LILRBs (2019) (0)
- 3P049 Revised CHARMM carbohydrate force field for improved description of conformational diversity of N-glycans(01A. Protein: Structure,Poster) (2013) (0)
- 1P211 Cholesterols affect to the association of the transmembrane region of Amyloid Precursor Protein in the raft(13B. Biological & Artificial membrane: Dynamics,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 2P120 An accurate modeling of the protein-membrane complex structures(The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- 3P055 Improved Multi-Replica Metadynamics for Free Energy Calculations(01C. Protein: Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- Structural Ramifications of Spike Protein D614G Mutation in SARS-CoV-2 (2022) (0)
- Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase (2018) (0)
- Constructing new proton pathways in nitric oxide reductases (2014) (0)
- 2P042 Molecular dynamics study of transmembrane segments of MIRs(The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- 2P043 多剤排出トランスポーター AcrB の Motion-Tree による解析 Motion-Tree analysis of the multidrug transporter AcrB (2015) (0)
- 1P116 Molecular dynamics simulation Magnesium transporter MgtE(Membrane proteins,Oral Presentations) (2007) (0)
- Generalized-Ensemble MD Simulations of Helix-Coil Transition (2001) (0)
- Secondary structure of SH3 domain in denatured state (2001) (0)
- Salt Effects on Folding of a Helical Mini Protein Villin Headpiece Subdomain HP36 Studied by Generalized-Ensemble Simulations (2014) (0)
- Vibrational Spectroscopic Analysis of Aromatic Polyamide Reverse Osmosis Membranes (2017) (0)
- 2PT130 Large-scale conformational changes of SERCA analyzed by Motion Tree method(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- 3P058 Dynamics and Interactions of Macromolecules in the Bacterial Cytoplasm : All-atom Molecular Dynamics Study(01C. Protein: Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 3P-090 The dimer conformation of amyloid β precursor protein fragment in membrane(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- 1P-005 Novel Scoring Function for Discriminating the Native Fold of a Protein from Misfolded Decoys(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- Crystal structure of nitric oxide reductase complex with HQNO (2012) (0)
- Conformational transition of the Sec translocon induced by channel partner: A molecular dynamics study (2009) (0)
- Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation. (2023) (0)
- Highly Charged Proteins and Their Repulsive Interactions Antagonize Biomolecular Condensation (2023) (0)
- Exploring APP-C99 complexes in lipid bilayers and their role in Alzheimer's disease (2020) (0)
- Stability of Proteins in Cellular Environments (2013) (0)
- 2P081 Sequential data assimilation to single-molecule FRET photoncounting data by using molecular dynamics simulations(01E. Protein: Measurement & Analysis,Poster) (2013) (0)
- Molecular Dynamics Simulation of Ca^ ATPase of Sarcoplasmic Reticulum (2003) (0)
- 3G1446 Molecular dynamics simulation of outer mitochondrial membrane protein Tom20-presequence complex(3G Protein: Structure 4,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- 1P-011 Parameters related to intramolecular hydrogen bonds characterizing the protein native structure(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- Free energy calculations of DNA base stacking using Replica-Exchange Umbrella Sampling (2003) (0)
- 3G1534 A multi-dimensional umbrella sampling approach for structure prediction of transmembrane helical dimer(3G Protein: Structure 4,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- 1 1 Implementation of residue-level coarse-grained models in GENESIS for 2 large-scale molecular dynamics simulations 3 (2021) (0)
- 3P110 Conformational change of SERCA upon alternating protonation states in Ca^ -binding site(03. Membrane proteins,Poster) (2013) (0)
- Exploring the conformational dynamics of the disordered Lid region of HDM2 N-terminal domain with molecular dynamics simulation. (2023) (0)
- Building a Macro-mixing Dual-basin Go Model using the Multistate Bennett Acceptance Ratio (2020) (0)
- Atomic Structures of Ion Pumps (2008) (0)
- Exploring N-Glycan Conformers: Assessment of Enhanced Sampling Algorithms (2016) (0)
- 2P131 The solvent-accessible surface area of proteins is a key factor for hydration structure and dynamics in crowded environment(07. Water & Hydration & Electrolyte,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- The impact of inhibitor size and flexibility on the binding pathways to c-Src kinase (2022) (0)
- 29pWE-11 Molecular Dynamics Simulations of Calcium Pump in a Lipid Bilayer (2004) (0)
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What Schools Are Affiliated With Yuji Sugita?
Yuji Sugita is affiliated with the following schools:
