A handful of molecular docking tools have been extended to enable a covalent docking.
However, all of them face the challenge brought by the covalent bond between proteins and …

Docking calculations can accelerate drug discovery by predicting the bound poses of
ligands for a targeted protein. However, it is not clear which docking methods work best …

The formation of a covalent bond with the target is essential for a number of successful
drugs, yet tools for covalent docking without significant restrictions regarding warhead or …

Covalent inhibitors have received extensive attentions in the past few decades because of
their long residence time, high binding efficiency and strong selectivity. Therefore, it is …

Molecular recognition plays a fundamental role in all biological processes, and that is why
great efforts have been made to understand and predict protein–ligand interactions. Finding …

In the validation of protein− ligand docking protocols, performance is mostly measured
against native protein conformers, ie each ligand is docked into the protein conformation …

Increased interest in covalent drug discovery led to the development of computer programs
predicting binding mode and affinity of covalent inhibitors. Here we compare the …

In recent years, machine-learning-based scoring functions have significantly improved the
scoring power. However, many of these methods do not perform well in distinguishing the …

The prediction of protein–ligand interactions and their corresponding binding free energy is
a challenging task in structure-based drug design and related applications. Docking and …

A common strategy for virtual screening considers a systematic docking of a large library of
organic compounds into the target sites in protein receptors with promising leads selected …