Structure-based virtual screening relies on classical scoring functions that often fail to
reliably discriminate binders from nonbinders. In this work, we present a high-throughput …

Molecular docking and molecular dynamics (MD) are powerful tools used to investigate
protein-ligand interactions. Molecular docking programs predict the binding pose and affinity …

Common failures in predicting crystal structures of ligand-protein complexes are
investigated for three ligand-protein systems by a combined thermodynamic and kinetic …

Protein‐ligand interactions are a necessary prerequisite for signal transduction,
immunoreaction, and gene regulation. Protein‐ligand interaction studies are important for …

Protein-ligand interaction is an imperative subject in structure-based drug design and
protein function prediction process. Molecular docking is a computational method which …

The binding mode prediction is of great importance to structure-based drug design. The
discrimination of various binding poses of ligand generated by docking is a great challenge …

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 …

We present a reliable and accurate solution to the induced fit docking problem for protein–
ligand binding by combining ligand-based pharmacophore docking, rigid receptor docking …

Computational drug discovery methods provide valuable insights into the understanding of
protein–ligand interaction systems in a virtual manner. Molecular docking and …

AutoDock and Vina are two of the most widely used protein–ligand docking programs. The
fact that these programs are free and available under an open source license, also makes …