Glossary

Ab initio calculations:

Calculations that are performed using basic principles of quantum mechanics, without any experimental data or assumptions.

Density functional theory (DFT):

A computational method that uses the electronic density of a system to calculate properties such as energy, structure, and reactivity.

Force field:

A mathematical model used to describe the interactions between atoms or molecules in a system.

Molecular mechanics:

A method of calculating the energy and forces in a molecular system based on classical mechanics.

Quantum mechanics (QM):

A theory that describes the behavior of particles at the atomic and subatomic level, and is used to calculate properties such as energy and structure in chemical systems.

Molecular dynamics (MD):

A computational method that simulates the motion of atoms and molecules over time, based on classical mechanics and force field calculations.

Monte Carlo (MC) simulations:

A computational method that uses statistical sampling to simulate the behavior of a system, based on random input parameters.

Basis set:

A set of mathematical functions used to describe the wave function of electrons in a quantum mechanical calculation.

Gaussian function:

A mathematical function that describes the shape of a wave function in a quantum mechanical calculation.

Energy minimization:

A computational method used to find the lowest-energy configuration of a system, by adjusting the positions of the atoms or molecules until the energy is minimized.

Ab initio molecular dynamics:

A type of molecular dynamics simulation that uses ab initio calculations to describe the behavior of a system.

Hybrid method:

A computational method that combines two or more types of calculations, such as DFT and molecular mechanics, to improve accuracy.

Electrostatic potential:

The electric field generated by a charged particle, which can be used to describe the interactions between molecules in a system.

Non-bonded interaction:

Interactions between atoms or molecules that are not directly bonded to each other, such as van der Waals forces or electrostatic interactions.

Drug design

Docking:

A computational method that predicts the binding mode and affinity of a small molecule to a target protein.

Ligand:

A small molecule that binds to a target protein and modulates its activity.

Receptor:

A protein that binds to a ligand and mediates its biological activity.

Molecular dynamics simulations:

A computational method that simulates the motion of atoms and molecules over time to predict the behavior of a system.

Virtual screening:

A computational method that uses molecular docking or other techniques to identify potential drug candidates from a large database of compounds.

Pharmacophore:

A set of chemical features that are necessary for a ligand to bind to a receptor and produce a biological response.

Quantitative structure-activity relationship (QSAR):

A computational method that predicts the activity of a compound based on its chemical structure and the activity of similar compounds.

Homology modeling:

A computational method that predicts the structure of a protein based on its sequence similarity to a known protein structure.

Fragment-based drug design:

A method of drug design that involves the identification of small fragments that bind to a target protein and the subsequent assembly of these fragments into a larger molecule.

Lead optimization:

The process of modifying a lead compound to improve its potency, selectivity, pharmacokinetic properties, or other desirable characteristics.

Drug-likeness:

A set of physicochemical properties that are commonly found in approved drugs, used to evaluate the potential of a compound to become a drug.

Target validation:

The process of demonstrating that a target protein is biologically relevant and is a suitable target for drug discovery.