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Concept
Chemical space
Summary
Chemical space is a concept in cheminformatics referring to the property space spanned by all possible molecules and chemical compounds adhering to a given set of construction principles and boundary conditions. It contains millions of compounds which are readily accessible and available to researchers. It is a library used in the method of molecular docking.
A chemical space often referred to in cheminformatics is that of potential pharmacologically active molecules. Its size is estimated to be in the order of 1060 molecules. There are no rigorous methods for determining the precise size of this space. The assumptions used for estimating the number of potential pharmacologically active molecules, however, use the Lipinski rules, in particular the molecular weight limit of 500. The estimate also restricts the chemical elements used to be Carbon, Hydrogen, Oxygen, Nitrogen and Sulfur. It further makes the assumption of a maximum of 30 atoms to stay below 500 Daltons, allows for branching and a maximum of 4 rings and arrives at an estimate of 1063. This number is often misquoted in subsequent publications to be the estimated size of the whole organic chemistry space, which would be much larger if including the halogens and other elements. In addition to the drug-like space and lead-like space that are, in part, defined by the Lipinski's rule of five, the concept of known drug space (KDS), which is defined by the molecular descriptors of marketed drugs, has also been introduced. KDS can be used to help predict the boundaries of chemical spaces for drug development by comparing the structure of the molecules that are undergoing design and synthesis to the molecular descriptor parameters that are defined by the KDS.
As of July 2009, there were 49,037,297 organic and inorganic substances registered with the Chemical Abstracts Service, indicating that they have been reported in the scientific literature. Chemical libraries used for laboratory-based screening for compounds with desired properties are examples for real-world chemical libraries of small size (a few hundred to hundreds of thousands of molecules).
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