Glossary of computational drug discovery terms
Short, accurate definitions of the terms you meet in docking, molecular dynamics, QSAR and ADME work.
ADME
Absorption, distribution, metabolism and excretion, the processes that determine how a compound behaves in the body. Learn more
Applicability domain
The chemical space in which a QSAR model can make reliable predictions. Learn more
Binding site
The region of a protein where a ligand binds, also called the active site or pocket.
Docking score
A numerical estimate of how favourable a ligand pose is, used to rank compounds. Learn more
Equilibration
The stage before production MD in which temperature, pressure and density are stabilised. Learn more
Force field
A set of equations and parameters describing the potential energy of atoms in a simulation, such as CHARMM36m or AMBER. Learn more
Free energy landscape (FEL)
A map of the energy of conformational states sampled in a simulation. Learn more
GROMACS
A widely used open-source software package for molecular dynamics simulations. Learn more
Grid box
The 3D search region in which a docking program places the ligand.
Homology modelling
Building a 3D protein model from its sequence using a related protein of known structure as a template. Learn more
Ligand
A small molecule that binds to a protein or other biomolecule. Learn more
Lipinski's rule of five
A drug-likeness guideline based on molecular weight, logP and hydrogen-bond donors and acceptors. Learn more
MM/GBSA
A faster variant of MM/PBSA that uses the Generalised Born model for solvation. Learn more
MM/PBSA
An end-state method that estimates binding free energy from MD snapshots using a Poisson–Boltzmann solvation model. Learn more
Molecular docking
A computational method that predicts the binding pose and approximate affinity of a ligand in a protein binding site. Learn more
Molecular dynamics (MD)
A simulation that follows the motion of atoms over time using classical physics, used to test stability and flexibility of biomolecular systems. Learn more
NVT and NPT ensembles
Simulation conditions with constant volume and temperature (NVT) or constant pressure and temperature (NPT). Learn more
PCA (principal component analysis)
A method that extracts the dominant collective motions from an MD trajectory. Learn more
PDB (Protein Data Bank)
A public database of experimentally determined 3D structures of proteins and other biomolecules.
Periodic boundary conditions
A simulation technique that treats the box as repeating in all directions to avoid edge effects.
Pose
A specific position and orientation of a ligand in a binding site.
Production run
The unrestrained MD simulation from which data is collected for analysis. Learn more
Protonation state
Which atoms of a molecule carry a proton at a given pH, affecting charge and hydrogen bonding. Learn more
QSAR
Quantitative structure–activity relationship, a statistical model linking chemical structure to biological activity. Learn more
RMSD
Root-mean-square deviation, a measure of how far a structure moves from a reference over time. Learn more
RMSF
Root-mean-square fluctuation, the flexibility of each residue during a simulation. Learn more
Radius of gyration (Rg)
A measure of how compact a protein is during a simulation. Learn more
Receptor
The protein or macromolecule that a ligand binds to.
Redocking
Docking the co-crystallised ligand back into its own structure to validate a docking protocol. Learn more
SASA
Solvent-accessible surface area, how much of a molecule is exposed to solvent. Learn more
SMILES
A text notation for describing the structure of a chemical molecule. Learn more
Trajectory
The recorded series of atomic positions over time produced by an MD simulation. Learn more
Virtual screening
Computational searching of compound libraries for molecules likely to bind a target. Learn more
ZINC20
A free public database of commercially available compounds for virtual screening. Learn more