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 …

Molecular docking is a process through which small molecules are docked into the
macromolecular structures for scoring its complementary values at the binding sites. It is a …

The General AMBER Force Field (GAFF) has been broadly used by researchers all over the
world to perform in silico simulations and modelings on diverse scientific topics, especially in …

Molecular docking has become an increasingly important tool for drug discovery. In this
review, we present a brief introduction of the available molecular docking methods, and their …

Binding free energy calculations based on molecular simulations provide predicted affinities
for biomolecular complexes. These calculations begin with a detailed description of a …

Improved rational drug design methods are needed to lower the cost and increase the
success rate of drug discovery and development. Alchemical binding free energy …

Accelerating the drug discovery process requires predictive computational protocols
capable of reducing or simplifying the synthetic and/or combinatorial challenge. Docking …

Accurate prediction of the absolute or relative protein–ligand binding affinity is one of the
major tasks in computer-aided drug design projects, especially in the stage of lead …

Many limitations of current computer-aided drug design arise from the difficulty of reliably
predicting the binding affinity of a small molecule to a biological target. There is thus a strong …

A strategy in drug design is to consider enhancing the affinity of lead molecules with
structural modifications that displace water molecules from a protein binding site. Because …