Computer-aided drug design (CADD) is an emerging field that has drawn a lot of interest
because of its potential to expedite and lower the cost of the drug development process …

Docking methodology aims to predict the experimental binding modes and affinities of small
molecules within the binding site of particular receptor targets and is currently used as a …

Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …

Molecular docking is a widely-used computational tool for the study of molecular recognition,
which aims to predict the binding mode and binding affinity of a complex formed by two or …

The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …

Understanding the ruling principles whereby protein receptors recognize, interact, and
associate with molecular substrates and inhibitors is of paramount importance in drug …

Abstract The cytochrome P450 (P450) enzymes first attracted interest because of their
relevance to the metabolism of drugs, steroids, and carcinogens. Collectively, the 57 human …

Consensus-scoring methods are commonly used with molecular docking in virtual screening
campaigns to filter potential ligands for a protein target. Traditional consensus methods …

Protein-ligand docking is currently an important tool in drug discovery efforts and an active
area of research that has been the subject of important developments over the last decade …

One approach to incorporate protein flexibility in molecular docking is the use of an
ensemble consisting of multiple protein structures. Sequentially docking each ligand into a …