Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest–Host Systems

• Published in: Journal of chemical theory and computation Vol. 16; no. 12; pp. 7721 - 7734
• Main Authors: Öhlknecht, Christoph, Perthold, Jan Walther, Lier, Bettina, Oostenbrink, Chris
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 08.12.2020
• Subjects: Binding sites; Free energy; Fullerenes - chemistry; Ligands; Molecular dynamics; Molecular Dynamics Simulation; Perturbation; Proteins; Static Electricity; Thermodynamics

Currently, two different methods dominate the field of biomolecular free-energy calculations for the prediction of binding affinities. Pathway methods are frequently used for large ligands that bind on the surface of a host, such as protein–protein complexes. Alchemical methods, on the other hand, a...