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.

Abstract excerpt

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and...

Topics

• Cytochrome-c Peroxidase
• Ligands
• Molecular Dynamics Simulation
• Mutation
• Saccharomyces cerevisiae
• Solvents
• Static Electricity
• Thermodynamics
• Thiazoles
• Water