Representation of chemical structures

At the root of applications for substructure and similarity searching, reaction retrieval, synthesis planning, drug discovery, and physicochemical property prediction is the need for a machine-readable representation of a structure. Systematic nomenclature is unsuitable, and notations and fragment codes have been superseded, except in certain specific applications. Connection tables are widely used, but there is no formal standard. Recently the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) has started to attract interest. This review also summarizes the representation of chemical reactions and three-dimensional structures. (C) 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 557-579 DOI:10.1002/wcms.36