Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

Rigorous physics-based methods to calculate binding free energies of protein–ligand
complexes have become a valued component of structure-based drug design. Relative and …

Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-
physical (alchemical) thermodynamic cycles have shown great promise for structure-based …

Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations
are key tools in both improving our understanding of a wide variety of biological processes …

The recent advances in relative protein–ligand binding free energy calculations have shown
the value of alchemical methods in drug discovery. Accurately assessing absolute binding …

Computational techniques see widespread use in pharmaceutical drug discovery, but
typically prove unreliable in predicting trends in protein-ligand binding. Alchemical free …

Free-energy calculations have seen increased usage in structure-based drug design.
Despite the rising interest, automation of the complex calculations and subsequent analysis …

Underpinning all drug discovery projects is the interaction between a drug and its target,
usually a protein. Thus, improved methods for predicting the magnitude of protein–ligand …

Absolute binding free energy calculations with explicit solvent molecular simulations can
provide estimates of protein-ligand affinities, and thus reduce the time and costs needed to …

Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …