Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …

Structure-based virtual screening (VS) is a widely used approach that employs the
knowledge of the three-dimensional structure of the target of interest in the design of new …

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 …

Motivation Protein–peptide interactions mediate a wide variety of cellular and biological
functions. Methods for predicting these interactions have garnered a lot of interest over the …

Highlights•Structure-based strategies allow more-specific targeting of protein–protein
interactions (PPIs).•Interfering peptides (IPs) become a promising alternative to small …

A significant number of protein–protein interactions (PPIs) are mediated through the
interactions between proteins and peptide segments, and therefore determination of protein …

Binding free energy calculations that make use of alchemical pathways are becoming
increasingly feasible thanks to advances in hardware and algorithms. Although relative …

The SARS-CoV-2 viral spike protein S receptor-binding domain (S-RBD) binds ACE2 on
host cells to initiate molecular events, resulting in intracellular release of the viral genome …

Accurate calculation of protein–protein binding free energy is of great importance in
biological and medical science, yet it remains a hugely challenging problem. In this work, we …

Background The WRKY transcription factors are a class of DNA-binding proteins involved in
diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome …