Abstract Background Molecular Dynamics (MD) simulations of protein complexes suffer from
the lack of specific tools in the analysis step. Analyses of MD trajectories of protein …

Structurally conserved residues at protein–protein interfaces correlate with the experimental
alanine-scanning hot spots. Here, we investigate the organization of these conserved …

Protein–protein interactions are implicated in the pathogenesis of many diseases and are
therefore attractive but challenging targets for drug design. One of the challenges in …

What conformations do protein molecules populate in solution? Crystallography provides a
high-resolution description of protein structure in the crystal environment, while NMR …

Reliably pinpointing which specific amino acid residues form the interface (s) between a
protein and its binding partner (s) is critical for understanding the structural and …

Protein–protein interactions, particularly weak and transient ones, are often mediated by
peptide recognition domains. Characterizing the interaction interface of domain–peptide …

Proteins undergo dynamic interactions with carbohydrates, lipids and nucleotides to form
catalytic cores, fine‐tuned for different cellular actions. The study of dynamic interactions …

A modification of the MM-PBSA technique for calculating binding affinities of biomolecular
complexes is presented. Classical molecular dynamics is used to explore the motion of the …

Protein recognition is one of the most challenging and intriguing problems in structural
biology. Despite all the available structural, sequence and biophysical information about …

Protein–ligand interactions taking place far away from the active site, during ligand binding
or release, may determine molecular specificity and activity. However, obtaining information …