Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …

Molecular recognition, which is the process of biological macromolecules interacting with
each other or various small molecules with a high specificity and affinity to form a specific …

NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Introduction: The molecular mechanics energies combined with the Poisson–Boltzmann or
generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods …

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

Recently, deep neural network (DNN)-based drug–target interaction (DTI) models were
highlighted for their high accuracy with affordable computational costs. Yet, the models' …

Solvation free energies can now be calculated precisely from molecular simulations,
providing a valuable test of the energy functions underlying these simulations. Here we …

Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …

We review insights from computational studies of affinities of ligands binding to proteins. The
power of structural biology is in translating knowledge of protein structures into insights …