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In biochemistry, a binding site is a region on a protein or piece of DNA or RNA to which ligands (specific molecules and/or ions) may form a chemical bond. An equilibrium exists between unbound ligands and bound ligands.
The term saturation refers to the fraction of total binding sites that are occupied at any given time. When more than one type of ligand can bind to a binding site, competition ensues.
Binding sites are often an important component of the functional characterization of biomolecules. For example, the characterization of the binding site of a substrate to an enzyme is essential to model the reaction mechanism responsible for the chemical change from substrate to product.
Binding sites on proteins can sometimes recognize other proteins. When a binding site of one protein identifies with another protein's surface, a non-covalent bond is formed between the two polypeptide (peptide) chains and a combined new protein is formed.
A more specific type of binding site is the transcription factor binding site present on DNA. Binding sites also exist on antibodies as specifically coded regions that bind antigens based upon their structure. Several supervised Machine learning models and applications where suggested to identify the binding sites 
- Alberts B, Bray D, Hopkin K, Johnson AD, Lewis J, Raff M, Roberts K, Walter P. (2010) Essential Cell Biology third edition.
- Binding Site - definition from Biology-Online.org
- Grau J., Ben-Gal I., Posch S., Grosse I.(2006. "VOMBAT: Prediction of Transcription Factor Binding Sites using Variable Order Bayesian Trees," (PDF). Nucleic Acids Research, vol. 34, issue W529–W533, 2006.
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