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Glossary of Terms

Target – a functional biomolecule (typically a protein) that has been identified as a potential “target” for small molecule therapeutics.

Ligand – a small molecule that binds a Target.

Monomer – BindingDB’s internal term for a Ligand. The term is used to distinguish small molecule ligands from Polymers, such as proteins and nucleic acids.

Polymer – a large molecule of repeating structural units linked by covalent bonds.  BindingDB uses this term for protein and nucleic acid targets.

Sequence – an ordered list of units in a molecule.  This can be the amino acid sequence of a protein or thea nucleic acid sequence of a DNA molecule, for example. 

Substrate – The reactant which is consumed during a catalytic or enzymatic reaction.

Competitor – a small molecule which binds to a protein by competing with its natural substrate.

IC50 - the concentration of ligand that reduces enzyme activity by 50% in a given assay.

KD – dissociation constant; the concentration of ligand that gives even odds that a given protein molecule has a ligand bound.

KI - For enzyme inhibitors, this is the inhibition constant, essentially the dissociation constant KD

EC50 - The concentration of compound that generates a half-maximal response in a given assay.

∆G – Gibbs free energy change associated with a chemical reaction, here a binding reaction

∆H – change in enthalpy associated with a chemical reaction, here a binding reaction.

∆S – change in enthropy associated with a chemical reaction, here a binding reaction.

FDA Drugs – small molecules approved by the Food and Drug Administration (FDA) for use against a particular disease.

SMILES - Simplified Molecular Input Line Entry Specification, a way to represent a 2D molecular structure as a compact string of text.

Het List – hetero atoms in a PDF file, which may correspond to a bound Ligand.

2D and 3D SDfiles – Downloadable compund/data files in Structure Data File (SDF) a format with either flat (2D) or computed 3D coordinates.

CSV file – comma separated value, a file format for various types of tables.

Swiss-Prot – an annotated protein database.

UniProt - the Universal Protein resource, a central repository of protein data created by combining the Swiss-Prot, TrEMBL and PIR-PSD databases

PubMed - a free database accessing the MEDLINE database of citations, abstracts and some full text articles on life sciences and biomedical topics.

PubChem - a database of chemical molecules maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine.

ITC - Isothermal titration calorimetry (ITC) is a physical technique used to determine the thermodynamic  parameters (∆G, ∆H, ∆S )of chemical reactions, including binding reactions, and often used to study the binding of small molecules to protein targets.

Substructure search – a search for small molecules containing a user-specified chemical fragment. For example, one might search for compounds containing a phenol substructure.

Virtual screening / similarity search – a general term for a variety of methods that identify similarities between small molecules.  BindingDB provides these tools to help identify the compounds in your own compound catalog that are most likely to be active against a desired target.