AbstractThe field of chemoinformatics makes use of a great number of different computational algorithms from mathematics and computer science as well as algorithms that are defined explicitly for challenges specific to chemoinformatics. This article provides an overview of algorithms and algorithmic complexity together with a review of common algorithmic design paradigms. These approaches are then given context with a set of relevant examples from chemoinformatics with definitions of the algorithms and, where relevant, graphical explanations. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 716‐726 DOI: 10.1002/wcms.42This article is categorized under: Computer and Information Science > Chemoinformatics