End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
Introduction: The molecular mechanics energies combined with the Poisson–Boltzmann or
generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods …
generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods …
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 …
Ligand-binding affinity estimates supported by quantum-mechanical methods
One of the largest challenges of computational chemistry is calculation of accurate free
energies for the binding of a small molecule to a biological macromolecule, which has …
energies for the binding of a small molecule to a biological macromolecule, which has …
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 …
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 …
A general picture of cucurbit [8] uril host–guest binding
Describing, understanding, and designing complex interaction networks within
macromolecular systems remain challenging in modern chemical research. Host–guest …
macromolecular systems remain challenging in modern chemical research. Host–guest …
The SAMPL4 host–guest blind prediction challenge: an overview
Prospective validation of methods for computing binding affinities can help assess their
predictive power and thus set reasonable expectations for their performance in drug design …
predictive power and thus set reasonable expectations for their performance in drug design …
On the use of interaction entropy and related methods to estimate binding entropies
V Ekberg, U Ryde - Journal of Chemical Theory and Computation, 2021 - ACS Publications
Molecular mechanics combined with Poisson–Boltzmann or generalized Born and solvent-
accessible area solvation energies (MM/PBSA and MM/GBSA) are popular methods to …
accessible area solvation energies (MM/PBSA and MM/GBSA) are popular methods to …
Using dispersion-corrected density functional theory to understand supramolecular binding thermodynamics
J Antony, R Sure, S Grimme - Chemical Communications, 2015 - pubs.rsc.org
A recently published theoretical approach employing a nondynamic structure model using
dispersion-corrected density functional theory (DFT-D3) to calculate equilibrium free …
dispersion-corrected density functional theory (DFT-D3) to calculate equilibrium free …