The ability to computationally predict protein-small molecule binding affinities with high
accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial …

Changes in free energy provide valuable information for molecular recognition, including
both ligand–receptor binding thermodynamics and kinetics. Umbrella sampling (US), a …

Approaches for computing small molecule binding free energies based on molecular
simulations are now regularly being employed by academic and industry practitioners to …

Accurately predicting the binding affinities of small organic molecules to biological
macromolecules can greatly accelerate drug discovery by reducing the number of …

Abstract Genistein (GEN), an isoflavone, exhibits wide array of biological activities such as
antioxidant, anti-inflammatory, cardioprotective and neuroprotective effects. However …

Obtaining a detailed description of how active site flap motion affects substrate or ligand
binding will advance structure-based drug design (SBDD) efforts on systems including the …

Accurately predicting receptor–ligand binding free energies is one of the holy grails of
computational chemistry with many applications in chemistry and biology. Many successes …

Self-association of α-synuclein peptides into oligomeric species and ordered amyloid fibrils
is associated with Parkinson's disease, a progressive neurodegenerative disorder. In …

The prediction of (un) binding rates and free energies is of great significance to the drug
design process. Although many enhanced sampling algorithms and approaches have been …

ApxII is a vaccine antigen used to protect against porcine contagious pleuropneumonia,
which is a significant threat to the pig industry. Here, we aimed to improve the proteolytic …