It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in
nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules …

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 …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

Highlights•High-throughput docking of small molecules is very successful in hit identification,
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …

The recent appearance of COVID-19 virus has created a global crisis due to unavailability of
any vaccine or drug that can effectively and deterministically work against it. Naturally …

Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-
physical (alchemical) thermodynamic cycles have shown great promise for structure-based …

Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Halogen atoms have been at the center of many rational medicinal chemistry applications in
drug design. While fluorine and chlorine atoms are often added to enhance physicochemical …

Molecular dynamics (MD) simulations are widely applied to estimate absolute binding free
energies of protein–ligand and protein–protein complexes. A routinely used method for …

Alchemical free energy simulations have long been utilized to predict free energy changes
for binding affinity and solubility of small molecules. However, while the theoretical …