A working glossary for
computational drug discovery

3D-QSAR is a class of computational modeling techniques that correlate the three-dimensional structural properties of chemical compounds with their...

ADMET stands for Absorption, Distribution, Metabolism, Excretion, and Toxicity.

Bioisosteres are chemical substituents or groups with similar physical or chemical properties that produce broadly similar biological effects when...

Biologics, also known as biological drugs, are therapeutic products derived from living organisms, including humans, animals, and microorganisms.

Chemical fingerprints are compact, computer-readable representations of molecular structures, typically encoded as binary strings or bit vectors.

A chemical library is a collection of stored chemicals that are used in high-throughput screening or industrial manufacturing.

Chemical reactivity refers to the propensity of a molecule or functional group to undergo chemical transformation in the presence of other substances or...

Chemical space refers to the vast and theoretically infinite universe of all possible chemical compounds, including both known and hypothetical molecules.

Cheminformatics, also known as chemical informatics or chemoinformatics, is the field of science that combines chemistry with computer science to process...

Clustering analysis is a statistical technique used to group similar objects into clusters such that objects within the same cluster are more similar to...

Covalent Docking is a computational technique used to predict the binding mode of covalent ligands to their target proteins.

De novo drug design is a computational approach used to create novel drug-like molecules from scratch.

Density Functional Theory (DFT) is a quantum mechanical method used to investigate the electronic structure of atoms, molecules, and condensed phases.

Molecular docking is a computational technique used to predict the preferred orientation of a ligand to a target (usually to a pre-defined site).

Drug resistance is the reduction in effectiveness of a drug in curing a disease or condition, often due to genetic mutations or adaptive changes in the...

An Electrostatic Potential (ESP) map is a visual representation of the electrostatic potential generated by a molecule in three-dimensional space.

Energy minimization is a computational technique used to find the lowest energy conformation of a molecular structure by adjusting the positions of its...

Ensemble docking is a computational technique used in drug discovery to account for the flexibility and dynamic nature of protein structures when...

Ensemble-Based Virtual Screening (EB-VS) uses docking against multiple conformations of a target protein—often derived from molecular dynamics...

Epigenetic targets are proteins and enzymes that regulate gene expression through reversible modifications to DNA, histones, or associated proteins...

Force fields are mathematical models used to describe the potential energy of a system of atoms or molecules.

Fragment-Based Drug Design (FBDD) is a method in drug discovery where chemical fragments up to 17 heavy atoms are used as starting points for developing...

Free energy calculations are used to estimate changes in free energy associated with molecular processes, such as ligand binding, protein folding, and...

High-throughput screening (HTS) is an experimental technique that enables the rapid testing of thousands to millions of compounds for biological activity...

Hit-to-Lead (H2L) optimization is a critical phase in the drug discovery process where initial "hit" compounds, identified through high-throughput...

Homology modeling, also known as comparative modeling, is a computational technique used to predict the three-dimensional structure of a protein based on...

Ligands are molecules that bind to specific sites on a target protein.

For a given series, Ligand Efficiency (LE) can be used as a metric in drug discovery to evaluate the binding energy of a ligand relative to its size.

Lipophilicity refers to the chemical property of a molecule that describes its ability to dissolve in fats, oils, lipids, and non-polar solvents versus...

Metadynamics is an enhanced sampling technique used in molecular dynamics (MD) simulations to efficiently explore the free energy landscape of molecular...

MM/PBSA (Molecular Mechanics/Poisson–Boltzmann Surface Area) and MM/GBSA (Molecular Mechanics/Generalized Born Surface Area) are computational methods...

Molecular descriptors are quantitative representations of molecular properties that can be derived from the chemical structure of a compound.

Molecular Dynamics (MD) simulations is a computational technique used to study the physical movements of atoms over time.

Molecular Mechanics (MM) is a computational approach used to model the physical movements and interactions of atoms and molecules.

Pharmacophore modeling is used to identify and represent the essential features of a molecule that are necessary for binding or activity.

Polypharmacology is the concept of designing or identifying drugs that interact with multiple biological targets rather than a single specific target.

Protein-ligand interactions refer to the binding between a protein and a ligand, which can be a small molecule, peptide, or another protein.

Protein-protein interactions (PPIs) are the physical contacts established between two or more protein molecules as a result of biochemical events and/or...

Quantitative Structure-Activity Relationship (QSAR) is a computational technique that models the relationship between the chemical structure of compounds...

Quantum Mechanics/Molecular Mechanics (QM/MM) is a computational technique that combines quantum mechanical (QM) and molecular mechanical (MM) methods to...

Reactive oxygen species (ROS) are chemically reactive molecules that contain oxygen, such as superoxide anion (O₂⁻), hydrogen peroxide (H₂O₂), and...

Ligand design requires molecules to be synthetically accessible.

SMILES is a specification for describing the structure of chemical molecules using short ASCII strings.

Structure-Based Drug Design is a method of drug discovery that relies on the three-dimensional structure of a target protein obtained through techniques...

The therapeutic index (TI) is a quantitative measure that compares the amount of a therapeutic agent that causes the desired effect to the amount that...

Thermodynamic cycles are conceptual tools used in computational chemistry and drug discovery to relate different states of a molecular system through a...

WaterMap is a computational tool used in drug discovery to analyze the thermodynamic properties of water molecules within and around biological...