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 …

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 soil bacterium Bacillus subtilis is a model organism to investigate the formation of
biofilms, the predominant form of microbial life. The secreted protein BslA self-assembles at …

Calculating the binding free energy of integral transmembrane (TM) proteins is crucial for
understanding the mechanisms by which they recognize one another and reversibly …

Highlights•Docking developments aim at improvement of modeling macromolecular
complexes.•Challenges include proper accounting for conformational flexibility.•Docking …

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 …

Protein–protein interactions are the basis of many protein functions, and understanding the
contact and conformational changes of protein–protein interactions is crucial for linking the …

Protein-protein interaction plays an essential role in almost all cellular processes and
biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle …