Concepts and protocols for electrostatic free energies

Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study

(2014) Manjeet Kumar et al.   CHEMPHYSCHEM

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

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

An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

(2014) Yen-Lin Lin et al.   Journal of Chemical Theory and Computation

Classical Electrostatics for Biomolecular Simulations

(2013) G. Andrés Cisneros et al.   CHEMICAL REVIEWS

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

(2013) Gabriel J. Rocklin et al.   JOURNAL OF CHEMICAL PHYSICS

The Active Site Loop Modulates the Reorganization Energy of Blue Copper Proteins by Controlling the Dynamic Interplay with Solvent

(2013) Licia Paltrinieri et al.   Journal of Physical Chemistry Letters

Explaining why Gleevec is a specific and potent inhibitor of Abl kinase

(2013) Y.-L. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protonation and pK changes in protein–ligand binding

(2013) Alexey V. Onufriev et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Understanding the Surface Potential of Water

(2011) Shawn M. Kathmann et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Reorganization Energy in Cytochrome c is Controlled by the Accessibility of the Heme to the Solvent

(2011) Carlo Augusto Bortolotti et al.   Journal of Physical Chemistry Letters

Distinct Ligand Specificity of the Tiam1 and Tiam2 PDZ Domains

(2010) Tyson R. Shepherd et al.   BIOCHEMISTRY

Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases

(2010) Alexey Aleksandrov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Prediction of Reorganization Free Energies for Biological Electron Transfer: A Comparative Study of Ru-Modified Cytochromes and a 4-Helix Bundle Protein

(2010) Varomyalin Tipmanee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Tetracycline-Tet Repressor Binding Specificity: Insights from Experiments and Simulations

(2009) Alexey Aleksandrov et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the origin of the electrostatic potential difference at a liquid-vacuum interface

(2008) Edward Harder et al.   JOURNAL OF CHEMICAL PHYSICS

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

(2008) L. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA