Protein–protein interactions (PPIs) execute many fundamental cellular functions and have
served as prime drug targets over the last two decades. Interfering intracellular PPIs with …

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 …

Peptide-protein interactions are involved in various fundamental cellular functions and their
identification is crucial for designing efficacious peptide therapeutics. Recently, a number of …

Protein–peptide interactions are crucial in many cellular functions. Therefore, determining
the structure of protein–peptide complexes is important for understanding the molecular …

Abstract Structure determination of linear peptides of 5–50 amino acids in aqueous solution
and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel …

Protein interactions are key in vital biological processes. In many cases, particularly in
regulation, this interaction is between a protein and a shorter peptide fragment. Such …

Classical simulations of protein flexibility remain computationally expensive, especially for
large proteins. A few years ago, we developed a fast method for predicting protein structure …

Autophagy is crucial for maintaining cell homeostasis. However, the precise mechanism
underlying autophagy initiation remains to be defined. Here, we demonstrate that glutamine …

A large number of protein–protein interactions (PPIs) are mediated by the interactions
between proteins and peptide segments binding partners, and therefore determination of …

Highlights•We provide an overview of protein-peptide docking methods and their
applications.•Peptide docking tools can be divided on template-based, local and global …