Yuji Sugita
Orcid: 0000-0001-9738-9216
According to our database1,
Yuji Sugita
authored at least 28 papers
between 2010 and 2024.
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Bibliography
2024
SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations.
J. Comput. Chem., March, 2024
2023
Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study.
PLoS Comput. Biol., 2023
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer.
J. Comput. Chem., 2023
2022
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images.
PLoS Comput. Biol., December, 2022
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.
PLoS Comput. Biol., 2022
Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions.
J. Chem. Inf. Model., 2022
2021
Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins.
J. Chem. Inf. Model., 2021
Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.
J. Chem. Inf. Model., 2021
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems.
J. Comput. Chem., 2021
2020
J. Chem. Inf. Model., 2020
J. Comput. Chem., 2020
2019
J. Chem. Inf. Model., 2019
Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations.
J. Comput. Chem., 2019
2017
Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations.
J. Comput. Chem., 2017
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.
J. Comput. Chem., 2017
Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems.
J. Comput. Chem., 2017
2016
Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations.
Comput. Phys. Commun., 2016
2015
Replica state exchange metadynamics for improving the convergence of free energy estimates.
J. Comput. Chem., 2015
2014
Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers.
J. Comput. Chem., 2014
Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations.
J. Comput. Chem., 2014
Proceedings of the 21st European MPI Users' Group Meeting, 2014
2013
J. Comput. Chem., 2013
2012
Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase.
PLoS Comput. Biol., 2012
Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods.
J. Comput. Chem., 2012
2011
Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation.
J. Comput. Chem., 2011
2010
Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins.
BMC Bioinform., 2010