Descriptors Generation Using the CDK Toolkit and Web Services

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


This chapter illustrates the generation of molecular descriptors using CDK Descriptor Calculator, E‐DRAGON web service and OCHEM web service, and the quick visual inspection of correlations between descriptors and biological endpoints. Molecular descriptors are attributes of a molecule, representations derived from its structural information, typically numbers that codify features of the molecular structure. Molecular descriptors are classified according to the type of information they encode. Constitutional descriptors encompass global molecular properties such as the molecular weight, number of atoms, number of bonds, number of rotatable bonds, or the sum of atomic volumes. Fragment descriptors count the occurrence of functional groups and sub‐structures previously defined. Topological descriptors consider the molecular structure as a mathematical graph—and graph theory can then be applied to generate graph invariants that are used as descriptors. Geometrical descriptors that encode 3D features of molecules are called “3D descriptors” and require information on 3D atomic coordinates.
Original languageEnglish
Title of host publicationTutorials in Chemoinformatics
EditorsA. Varnek
PublisherJohn Wiley & Sons, Ltd
ISBN (Electronic)9781119161110
ISBN (Print)9781119137962
Publication statusPublished - 28 Jul 2017


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