Protein–protein interactions form central elements of almost all cellular processes.
Knowledge of the structure of protein–protein complexes but also of the binding affinity is of …

Recent success stories suggest that in silico protein–ligand binding free-energy calculations
are approaching chemical accuracy. However, their widespread application remains limited …

We reassess progress in the field of biomolecular modeling and simulation, following up on
our perspective published in 2011. By reviewing metrics for the field's productivity and …

Accurate absolute binding free-energy estimation in silico, following either an alchemical or
a geometrical route, involves several subprocesses and requires the introduction of …

We determined the effectiveness of absolute binding free energy (ABFE) calculations to
refine the selection of active compounds in virtual compound screening, a setting where the …

Quantitative evaluation of binding affinity changes upon mutations is crucial for protein
engineering and drug design. Machine learning‐based methods are gaining increasing …

Highlights•Binding free energy calculations are increasing used in drug design and
biotechnology.•We distinguish end-state methods, alchemical methods and pathway …

Calculating the standard binding free energies of protein–protein and protein–ligand
complexes from atomistic molecular dynamics simulations in explicit solvent is a problem of …

The spike protein of SARS-CoV-2 is known to interact with the human ACE2 protein via its
receptor binding domain (RBD). We have investigated the molecular nature of this …

Molecular docking excels at creating a plethora of potential models of protein–protein
complexes. To correctly distinguish the favorable, native-like models from the remaining …