Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent

Accurate Calculation of Solvation Free Energies in Supercritical Fluids by Fully Atomistic Simulations: Probing the Theory of Solutions in Energy Representation

(2015) Andrey I. Frolov   Journal of Chemical Theory and Computation

On the urea induced hydrophobic collapse of a water soluble polymer

(2015) Francisco Rodríguez-Ropero et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Finite-Size Effect on the Charging Free Energy of Protein in Explicit Solvent

(2014) Toru Ekimoto et al.   Journal of Chemical Theory and Computation

Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions

(2014) Shun Sakuraba et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Folding Dynamics of the Trp-Cage Miniprotein: Evidence for a Native-Like Intermediate from Combined Time-Resolved Vibrational Spectroscopy and Molecular Dynamics Simulations

(2013) Heleen Meuzelaar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Interaction-component analysis of the urea effect on amino acid analogs

(2013) Yasuhito Karino et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Folding and unfolding thermodynamics of the TC10b Trp-cage miniprotein

(2013) Charles A. English et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Molecular dynamics study on binding free energy of Azurin–Cytochrome c551 complex

(2012) Hiroaki Saito et al.   CHEMICAL PHYSICS LETTERS

Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation

(2012) Tomonori Kawakami et al.   JOURNAL OF CHEMICAL PHYSICS

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

(2012) Kazuhiro Takemura et al.   JOURNAL OF CHEMICAL PHYSICS

Regularizing Binding Energy Distributions and the Hydration Free Energy of Protein Cytochrome C from All-Atom Simulations

(2012) Valéry Weber et al.   Journal of Chemical Theory and Computation

Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction

(2012) M. Scian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Backbone and Side-Chain Contributions in Protein Denaturation by Urea

(2011) Deepak R. Canchi et al.   BIOPHYSICAL JOURNAL

Solvation effect on the structural change of a globular protein: A molecular dynamics study

(2011) Taku Mizukami et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Communication: Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c

(2011) Yasuhito Karino et al.   JOURNAL OF CHEMICAL PHYSICS

Calculation of Configurational Entropy with a Boltzmann–Quasiharmonic Model: The Origin of High-Affinity Protein–Ligand Binding

(2011) Kyle W. Harpole et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hydration Thermodynamics Using the Reference Interaction Site Model: Speed or Accuracy?

(2011) Andrey I. Frolov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Influence of water–protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

(2011) Dietmar Paschek et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2011) Satoshi Yasuda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Hydration property of globular proteins: An analysis of solvation free energy by energy representation method

(2010) Hiroaki Saito et al.   CHEMICAL PHYSICS LETTERS

End-point calculation of solvation free energy of amino-acid analogs by molecular theories of solution

(2010) Yasuhito Karino et al.   CHEMICAL PHYSICS LETTERS

Equilibrium Study of Protein Denaturation by Urea

(2010) Deepak R. Canchi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Roles of translational motion of water molecules in sustaining life

(2009) Masahiro Kinoshita   Frontiers in Bioscience-Landmark

Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations

(2009) Z. Gattin et al.   PROTEIN SCIENCE

Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation

(2008) Nobuyuki Matubayasi et al.   JOURNAL OF CHEMICAL PHYSICS

Variational and perturbative formulations of quantum mechanical/molecular mechanical free energy with mean-field embedding and its analytical gradients

(2008) Takeshi Yamamoto   JOURNAL OF CHEMICAL PHYSICS

Computation of the free energy change associated with one-electron reduction of coenzyme immersed in water: A novel approach within the framework of the quantum mechanical/molecular mechanical method combined with the theory of energy representation

(2008) Hideaki Takahashi et al.   JOURNAL OF CHEMICAL PHYSICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

The Trp-cage: optimizing the stability of a globular miniprotein

(2008) B. Barua et al.   PROTEIN ENGINEERING DESIGN & SELECTION