Advances in Chemical Biology

0502892 - ÚMG 2019 RIV CZ eng M - Monography Chapter
Novotný, Jiří - Svozil, Daniel
Small Overview of Molecular Descriptors.
Advances in Chemical Biology. Praha: OPTIO CZ, 2019 - (Bartůněk, P.), s. 159-165. ISBN 978-80-88011-03-3
R&D Projects: GA MŠMT LO1220
Institutional support: RVO:68378050
Keywords : cheminformatics * structure * physico-chemical descriptors * theoretical descriptors
OECD category: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

If we want to study molecules by mathematical and statistical methods, it is essential to numerically characterize their structure. For that, molecular descriptors are used. Formally, descriptors are described as follows 1: ´The molecular descriptor is the final result of a logic and mathematical procedure which transforms chemical information encoded within a symbolic representation of a molecule into a useful number or the result of some standardized experiment.´. Simply said, descriptors try to extract and summarize information encoded in the structure of molecules to form which is mathematically graspable, i.e. typically into a number, vector, or matrix. The example of a descriptor is a molecular weight or a number of heavy (non-hydrogen) atoms. Besides using descriptors as an input to downstream methods, they are important in quantifying distance or similarity between molecules 2. For descriptors, generally two principles apply: 1) physico-chemical and biological properties of a molecule are related to its structure and 2) structurally similar molecules will have similar physico-chemical properties.
Descriptors play a fundamental role in chemoinformatics and they are derived using e.g. graph and information theory or by physical, quantum and organic chemistry. There are two main groups of chemoinformatics methods where descriptors are used 3: QSAR (Quantitative Structure-Activity Relationship) and QSPR (Quantitative Structure-Property Relationship). These methods are widely used in many fields, e.g. in medicinal chemistry, computer-aided drug design, toxicology, analytical chemistry or environmental studies.
Descriptors can be divided into the two main groups 1. The first is based on experimental measurements and generally contains the physico-chemical descriptors. The second group contains theoretical descriptors, which are derived from the symbolic representation of a molecule and further divided according to the dimensionality of the representation. Descriptors are, thus, divided into 0D, 1D, 2D, 3D and 4D descriptors and these individual types will be presented in the separate chapters. However, some descriptors belong to more than one class or may not have a clearly defined class, so it is necessary to take this classification rather indicatively. In general, however, the higher dimensional descriptor is, the more expensive it is to be computed, but it usually covers more chemical information..

Permanent Link: http://hdl.handle.net/11104/0295013