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 …

Docking has become an indispensable approach in drug discovery research to predict the
binding mode of a ligand. One great challenge in docking is to efficiently refine the correct …

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 …

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 …

The accurate prediction of a ligand–protein complex structure is important for computer-
assisted drug development. Although many docking methods have been developed over the …

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

Introduction: The volume of three-dimensional structural information of macromolecules and
the number of computational tools to predict binding modes and affinities of molecular …

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 …

In the field of medicinal chemistry there is increasing focus on identifying key proteins whose
biochemical functions can firmly be linked to serious diseases. Such proteins become …

As one of the most popular computational approaches in modern structure-based drug
design, molecular docking can be used not only to identify the correct conformation of a …