Predicting binding free energies: frontiers and benchmarks
Binding free energy calculations based on molecular simulations provide predicted affinities
for biomolecular complexes. These calculations begin with a detailed description of a …
for biomolecular complexes. These calculations begin with a detailed description of a …
Overview of the SAMPL5 host–guest challenge: Are we doing better?
The ability to computationally predict protein-small molecule binding affinities with high
accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial …
accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial …
Assessment of binding affinity via alchemical free-energy calculations
M Kuhn, S Firth-Clark, P Tosco, ASJS Mey… - Journal of Chemical …, 2020 - ACS Publications
Free-energy calculations have seen increased usage in structure-based drug design.
Despite the rising interest, automation of the complex calculations and subsequent analysis …
Despite the rising interest, automation of the complex calculations and subsequent analysis …
Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database
G Duarte Ramos Matos, DY Kyu… - Journal of Chemical & …, 2017 - ACS Publications
Solvation free energies can now be calculated precisely from molecular simulations,
providing a valuable test of the energy functions underlying these simulations. Here we …
providing a valuable test of the energy functions underlying these simulations. Here we …
Overview of the SAMPL6 host–guest binding affinity prediction challenge
Accurately predicting the binding affinities of small organic molecules to biological
macromolecules can greatly accelerate drug discovery by reducing the number of …
macromolecules can greatly accelerate drug discovery by reducing the number of …
Automated adaptive absolute binding free energy calculations
Alchemical absolute binding free energy (ABFE) calculations have substantial potential in
drug discovery, but are often prohibitively computationally expensive. To unlock their …
drug discovery, but are often prohibitively computationally expensive. To unlock their …
Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge
In the recent SAMPL5 challenge, participants submitted predictions for cyclohexane/water
distribution coefficients for a set of 53 small molecules. Distribution coefficients (log D) …
distribution coefficients for a set of 53 small molecules. Distribution coefficients (log D) …
Comparison of receptor–ligand restraint schemes for alchemical absolute binding free energy calculations
Alchemical absolute binding free energy calculations are of increasing interest in drug
discovery. These calculations require restraints between the receptor and ligand to restrict …
discovery. These calculations require restraints between the receptor and ligand to restrict …
Hydrophobe challenge: A joint experimental and computational study on the host–guest binding of hydrocarbons to cucurbiturils, allowing explicit evaluation of guest …
KI Assaf, M Florea, J Antony… - The Journal of …, 2017 - ACS Publications
The host–guest complexation of hydrocarbons (22 guest molecules) with cucurbit [7] uril was
investigated in aqueous solution using the indicator displacement strategy. The binding …
investigated in aqueous solution using the indicator displacement strategy. The binding …
The role of water in host-guest interaction
One of the main applications of atomistic computer simulations is the calculation of ligand
binding free energies. The accuracy of these calculations depends on the force field quality …
binding free energies. The accuracy of these calculations depends on the force field quality …