Cheminformatics can be defined as the application of computer science methods to solve chemical problems. This includes techniques to store, process, and manipulate chemical data. The field focuses on small molecules (chemical compounds), and one of the main application of Cheminformatics is finding novel structures that are potential drug candidates.

Chemical compounds can be represented by line notations (like SMILES and InChI), and various algorithms exist to compute 2D structure layout and 3D conformation of compounds. Moreover, a broad range of numerical descriptors (e.g., physico-chemical descriptors) exist to calculate compound properties based on their structure. Another important feature type is structural fragments, hence, graph mining tools can be applied to mine frequent sub-graphs in compound datasets (link to graph mining).

An important domain within Cheminformatics is (Q)SAR ((Quantitative) structure activity relationship) modelling for analyzing and predicting the biological or chemical activity of compounds. One important application area of cheminformatics is the field of Predictive Toxicology.