Table 1.

Computer-aided techniques used in drug design and discovery.

Technique	Roles in drug design and discovery
Docking	Predict binding mode and approximate binding energy of a compound to a target
Structure-based virtual screening	Identify active compounds for a specific target from a chemical library based on docking techniques
Pharmacophore modeling	Perceive and provide description of molecular features necessary for molecular recognition of a ligand by a biological macromolecule
Ligand-based virtual screening	Identify active compounds for a specific target from a chemical library based on pharmacophore modeling techniques
Homology modeling	Build a 3D structure for structure-based drug design for a target for which no crystal structure is available, based on related protein 3D structures
Molecular dynamics	Molecular mechanics-based simulation to understand the dynamic behavior of proteins or other biological macromolecules, to analyze the flexibility of the drug target for structure-based drug design and/or to calculate the binding affinity of a compound to a target
2D quantitative structure–activity relationship	Finding a model that can be used to predict some property from the molecular structure of a compound
3D quantitative structure–activity relationship	Technique used to quantitatively predict the interaction between a molecule and the active site of a target; 3D conformation-derived information is utilized in this technique
Quantum mechanics	An electron-orbital-based approach based on first principles to optimize structures of ligands and even protein–ligand complexes, improve the accuracy of docking and calculate, for example, free-binding energy
Absorption, distribution, metabolism, elimination, and toxicity prediction	Prediction of absorption, distribution, metabolism, elimination and toxicity of chemical substances in the human body to avoid costly later-stage failures in drug development