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List of works by Hiraku Oshima

A highly efficient hybrid method for calculating the hydration free energy of a protein.

scientific article

A theoretical analysis on characteristics of protein structures induced by cold denaturation.

scientific article published in November 2009

Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition

scientific article

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

scientific article published on 28 October 2020

Characterization of experimentally determined native-structure models of a protein using energetic and entropic components of free-energy function

scientific article published on 29 June 2012

Crucial importance of the water-entropy effect in predicting hot spots in protein–protein complexes ⬇️

scientific article published on August 15, 2011

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

scientific article published on 21 August 2019

Effects of side-chain packing on the formation of secondary structures in protein folding.

scientific article published in February 2010

Effects of sugars on the thermal stability of a protein

scientific article

Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape

scientific article published on 26 August 2019

Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: comparison between hard-sphere solvent and water.

scientific article published in April 2015

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

scientific article

Mechanism of One-to-Many Molecular Recognition Accompanying Target-Dependent Structure Formation: For the Tumor Suppressor p53 Protein as an Example.

scientific article published on 19 October 2015

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

scientific article published in 2022

On the physics of multidrug efflux through a biomolecular complex.

scientific article published in November 2013

On the physics of thermal-stability changes upon mutations of a protein.

scientific 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

Replica-Exchange Methods for Biomolecular Simulations

scientific article published on 01 January 2019

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

scientific article published on 27 September 2019

Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects

scientific article

Statistical thermodynamics for functionally rotating mechanism of the multidrug efflux transporter AcrB.

scientific article published on 12 February 2015

Storage capacity and retrieval time of small-world neural networks

scientific article published on 26 September 2007

Structural Mechanisms Underlying Activity Changes in an AMPA-type Glutamate Receptor Induced by Substitutions in Its Ligand-Binding Domain

scientific article published on 01 October 2019

Structural stability of proteins in aqueous and nonpolar environments

scientific article published on 01 October 2012

Water based on a molecular model behaves like a hard-sphere solvent for a nonpolar solute when the reference interaction site model and related theories are employed.

scientific article published in July 2016

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