Molecular docking has been widely employed as a fast and inexpensive technique in the
past decades, both in academic and industrial settings. Although this discipline has now had …

Abstract Structure-based drug design uses three-dimensional geometric information of
macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric …

Abstract The Protein Data Bank (PDB) is the single global archive of experimentally
determined three-dimensional (3D) structure data of biological macromolecules. Since …

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 …

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 …

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 …

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 …

Structure-based virtual screening (VS) is a widely used approach that employs the
knowledge of the three-dimensional structure of the target of interest in the design of new …

Molecule docking has been regarded as a routine tool for drug discovery, but its accuracy
highly depends on the reliability of scoring functions (SFs). With the rapid development of …

Reports of successful applications of machine learning (ML) methods in structure-based
virtual screening (SBVS) are increasing. ML methods such as convolutional neural networks …