Basic ingredients of free energy calculations: A review

By Clara D. Christ, Alan E. Mark, W. V. van Gunsteren. Journal of Computational Chemistry, 2009

376 citations recorded by the source corpus.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration (2013, neutral): “, [1–5]).”
Predicting binding free energies: Frontiers and benchmarks (2016, methodology): “The second general approach computes the difference between the binding free energies of two different ligands for the same receptor, by computing the work of artificially converting one ligand into another, first in the bound state and then free in solution [24, 27, 114, 175].”
Umbrella sampling (2011, background): “5 , 6 Techniques are regularly being reviewed in the literature, with a few recent ones given in J Comput Chem 7 and in a themed issue of J Comput Chem in 2009.”
Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, background): “For further detailed theoretical background of free energy calculations, the reader is referred to [3,15,188,190,191].”
FreeSolv: A database of experimental and calculated hydration free energies, with input files (2014, positive): “Our approach to calculating these typically involves alchemical free energy calculations based on classical molecular dynamics (MD) simulations [5, 7, 29, 48], usually with a fixed-charge force field in explicit solvent.”