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WIREs Comput Mol Sci
Impact Factor: 8.127

Representation of chemical structures

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Abstract 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 Systematic nomenclature is unsuitable, and notations and fragment codes have been superseded, except in certain specific applications.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. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 557–579 DOI: 10.1002/wcms.36 This article is categorized under: Computer and Information Science > Chemoinformatics

A Wiswesser Line Notation.

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InfoChem spheres around reaction centers.

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Atom‐to‐atom mapping.

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Types of variation in Markush structures. (Reprinted with permission from Digital Chemistry, unpublished work)

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Mesomers with the same InChIKey but different newly enhanced Morgan algorithm (NEMA) keys. (Reprinted with permission from Symyx Technologies, unpublished work)

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Tautomers with different newly enhanced Morgan algorithm (NEMA) keys but the same InChIKeys. (Reprinted with permission from Symyx Technologies, unpublished work)

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National Cancer Institute Computer Aided Drug Design identifiers.

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Example of an IUPAC International Chemical Identifier (InChI) and InChIKey.

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MDL connection table organization.

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A redundant connection table.

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A Simplified Molecular Input Line Entry System notation.

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