We present an energy function for predicting binding free energies of protein–protein
complexes, using the three‐dimensional structures of the complex and unbound proteins as …

In a previous paper, we described a novel empirical free energy function that was used to
accurately predict experimental binding free energies for a diverse test set of 31 protein …

It is possible to accurately and economically predict change in protein-protein interaction
energy upon mutation (ΔΔG), when a high-resolution structure of the complex is available …

A long sought goal in the physical chemistry of macromolecular structure, and one directly
relevant to understanding the molecular basis of biological recognition, is predicting the …

Many functional proteins are at least partially disordered prior to binding. Although the
structural transitions upon binding of disordered protein regions can influence the affinity …

The accurate prediction of protein–protein complex geometries is of major importance to
ultimately model the complete interactome of interacting proteins in a cell. A major …

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

We report here a computationally fast protocol for predicting binding affinities of non-metallo
protein–ligand complexes. The protocol builds in an all atom energy based empirical …

A free energy function can be defined as a mathematical expression that relates
macroscopic free energy changes to microscopic or molecular properties. Free energy …

Understanding and predicting the energetics of protein–protein interactions is fundamental
to the structural modeling of protein complexes. Binding free energy can be approximated as …