Highlights•The first successfully designed and validated protein–protein interactions were
recently published.•Novel combinations of high-throughput experimental characterization …

The computer-based design of protein–protein interactions is a rigorous test of our
understanding of molecular recognition and an attractive approach for creating novel tools …

Computational design of protein–ligand interfaces finds optimal amino acid sequences
within a small-molecule binding site of a protein for tight binding of a specific small molecule …

Highlights•Many computationally designed protein–protein interactions were reported over
the past two years.•Recent design goals include heterodimers, homodimers …

Given the importance of protein–protein interactions for nearly all biological processes, the
design of protein affinity reagents for use in research, diagnosis or therapy is an important …

The design of proteins that bind to a specific site on the surface of a target protein using no
information other than the three-dimensional structure of the target remains a challenge …

The recognition process between a protein and a partner represents a significant theoretical
challenge. In silico structure-based drug design carried out with nothing more than the three …

Highlights•The recent progress in ligand-binding protein design is reviewed.•Combining
computational design with experimental screen gives successful results.•Success rate of …

Combinatorial libraries with restricted diversity can be used to rapidly map binding
energetics across protein interfaces. Shotgun scanning strategies have been used for …

The design of proteins that bind to a specific site on the surface of a target protein using no
information other than the three-dimensional structure of the target remains an outstanding …