Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

Protein–protein interactions form central elements of almost all cellular processes.
Knowledge of the structure of protein–protein complexes but also of the binding affinity is of …

Background Molecular docking studies on protein-peptide interactions are a challenging
and time-consuming task because peptides are generally more flexible than proteins and …

In sepsis, macrophage bacterial phagocytosis is impaired, but the mechanism is not well
elucidated. Extracellular cold-inducible RNA-binding protein (eCIRP) is a damage …

Motivation Binding-induced conformational changes challenge current computational
docking algorithms by exponentially increasing the conformational space to be explored. To …

Flexibility is often a key determinant of protein function. To elucidate the link between their
molecular structure and role in an organism, computational techniques such as molecular …

Highlights•Reviewed scoring schemes and conformational sampling for protein–protein
complex structure prediction.•Discussed the database for binding affinity of complexes and …

Extracellular cold-inducible RNA-binding protein (eCIRP) is an important damage-
associated molecular pattern (DAMP). Despite our understanding of the potentially harmful …

Protein-protein docking methods have been widely used to gain an atomic-level
understanding of protein interactions. However, docking methods that employ low-resolution …