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

Protein–protein assemblies act as a key component in numerous cellular processes. Their
accurate modeling at the atomic level remains a challenge for structural biology. To address …

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 …

Homology models have been used for virtual screening and to understand the binding mode
of a known active compound; however, rarely have the models been shown to be of …

We present an approach combining alchemical modifications and physical-pathway
methods to calculate absolute binding free energies. The employed physical-pathway …

Protein–protein docking typically consists of the generation of putative binding
conformations, which are subsequently ranked by fast heuristic scoring functions. The …

Accurate prediction and evaluation of protein–protein complex structures are of major
importance to understand the cellular interactome. Typically, putative complexes are …

Proteolysis targeting chimeras represent a class of drug molecules with a number of
attractive properties, most notably a potential to work for targets that, so far, have been in …

Cu, Zn superoxide dismutase (SOD1) is a 32 kDa homodimer that converts toxic oxygen
radicals in neurons to less harmful species. The dimerization of SOD1 is essential to the …

Protein–protein interactions are crucial in many biological processes. Therefore,
determining the structure of a protein–protein complex is valuable for understanding its …