The accurate design of new protein–protein interactions is a longstanding goal of
computational protein design. However, most computationally designed interfaces fail to …

The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of
protein Structure Prediction) experiments have demonstrated the power of community-wide …

To understand further, and to utilize, the interactions across protein-protein interfaces, we
carried out an analysis of the hydrogen bonds and of the salt bridges in a collection of 319 …

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 …

At the heart of protein–protein interactions are protein–protein interfaces where the direct
physical interactions occur. By developing and applying an efficient structural alignment …

Understanding how proteins encode ligand specificity is fascinating and similar in
importance to deciphering the genetic code. For protein–ligand recognition, the combination …

Motivations: Characterizing protein–protein interfaces and the hydrogen bonds is a first step
to better understand proteins' structures and functions toward high-resolution protein design …

Background Few existing protein-protein interface design methods allow for extensive
backbone rearrangements during the design process. There is also a dichotomy between …

Computational design of novel protein–protein interfaces is a test of our understanding of
protein interactions and has the potential to allow modification of cellular physiology …

We compare the geometric and physical–chemical properties of interfaces involved in
specific and non-specific protein–protein interactions in crystal structures reported in the …