Molecular docking is a computational method widely used in drug discovery. Due to the
inherent inaccuracies of molecular docking, visual inspection of binding modes is a crucial …

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 …

AutoDock Vina is arguably one of the fastest and most widely used open-source programs
for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks …

In structure-based drug design, scoring functions are often employed to evaluate protein–
ligand interactions. A variety of scoring functions have been developed so far, and thus …

Targeted protein degradation via “hijacking” of the ubiquitin-proteasome system using
proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality …

Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …

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 …

Computational approaches to drug discovery can reduce the time and cost associated with
experimental assays and enable the screening of novel chemotypes. Structure-based drug …

Molecular docking plays a significant role in early-stage drug discovery, from structure-
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …

Molecular docking is a widely used method to predict the binding modes of small-molecule
ligands to the target binding site. However, it remains a challenge to identify the correct …