In silico tools, such as molecular docking, are widely applied to study interactions and
binding affinity of biological activity of proteins and peptides. However, restricted sampling of …

Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations of …

Designing a reliable computational methodology to calculate protein: ligand standard
binding free energies is extremely challenging. The large change in configurational enthalpy …

Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

P450 TleB catalyzes the oxidative cyclization of the dipeptide N-methylvalyl-tryptophanol
into indolactam V through selective intramolecular C–H bond amination at the indole C4 …

Developing synthetically useful enzymatic reactions that are not known in biochemistry and
organic chemistry is an important challenge in biocatalysis. Through the synergistic merger …

Quantum computing holds substantial potential for applications in biology and medicine,
spanning from the simulation of biomolecules to machine learning methods for subtyping …

GPR84 is an orphan class AG protein-coupled receptor (GPCR) that is predominantly
expressed in immune cells and plays important roles in inflammation, fibrosis, and …

The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of
any biological system and yet, many aspects of its role remain elusive. Here, we simulate …

The prediction of drug–target binding and unbinding kinetics that occur on time scales
between milliseconds and several hours is a prime challenge for biased molecular …