Protein interactions are often accompanied by significant changes in conformation. We have
analyzed the relationships between protein structures and the conformational changes they …

Molecular docking programs play an important role in drug development and many well‐
established methods exist. However, there are two situations for which the performance of …

Many applications in protein engineering require optimizing multiple protein properties
simultaneously, such as binding one target but not others or binding a target while …

Highly accurate protein structure predictions by deep neural networks such as AlphaFold2
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …

The three key challenges addressed in our development of Specitope, a tool for screening
large structural databases for potential ligands to a protein, are to eliminate infeasible …

Conspectus The dynamics of protein binding pockets are crucial for their interaction
specificity. Structural flexibility allows proteins to adapt to their individual molecular binding …

Understanding and control of structures and rates involved in protein ligand binding are
essential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations …

A protein in its native, folded conformation creates a solvent-exposed (exterior) surface and
a solventexcluded (interior) surface (Figure 1). Enzyme active sites are most often found at …

Self-binding peptide (SBP) represents a novel biomolecular phenomenon spanning
between folding and binding. It is a structurally independent, short peptide segment within a …

To better understand the interplay between protein-protein binding and protein dynamics,
we analyzed molecular dynamics simulations of 17 protein-protein complexes and their …