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The Journal of Physical Chemistry Letters|March 14, 2026
Free Energy Calculation Method Based on Enhanced Sampling of Diverse Protein Conformations Predicted by Artificial IntelligenceToma Aoki, Ryuhei HaradaPhysical Chemistry Chemical Physics : PCCP|June 21, 2018
How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulationsRyuhei Harada, Yasuteru ShigetaJournal of Molecular Graphics & Modelling|September 12, 2018
Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiencyRyuhei Harada, Yasuteru ShigetaJournal of Chemical Information and Modeling|November 8, 2017
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational SearchesRyuhei Harada, Yasuteru ShigetaThe Journal of Physical Chemistry. B|June 9, 2011
Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation methodRyuhei Harada, Akio KitaoJournal of Chemical Theory and Computation|November 24, 2018
Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy CalculationsRyuhei Harada, Yasuteru ShigetaJournal of Chemical Information and Modeling|August 20, 2019
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling EfficiencyRyuhei Harada, Yasuteru ShigetaJournal of Chemical Theory and Computation|February 8, 2017
Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of ProteinsRyuhei Harada, Yasuteru ShigetaThe Journal of Chemical Physics|July 26, 2013
Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to generate conformational transition pathwayRyuhei Harada, Akio KitaoJournal of Chemical Theory and Computation|November 18, 2015
Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of ProteinsRyuhei Harada, Akio KitaoPageof 10